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ensembl-vep/INSTALL.pl at release/113 · Ensembl/ensembl-vep · GitHub
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perl","","=head1 LICENSE","","Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute","Copyright [2016-2024] EMBL-European Bioinformatics Institute","","Licensed under the Apache License, Version 2.0 (the \"License\");","you may not use this file except in compliance with the License.","You may obtain a copy of the License at",""," http://www.apache.org/licenses/LICENSE-2.0","","Unless required by applicable law or agreed to in writing, software","distributed under the License is distributed on an \"AS IS\" BASIS,","WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.","See the License for the specific language governing permissions and","limitations under the License.","","=cut","","=head1 CONTACT",""," Please email comments or questions to the public Ensembl"," developers list at \u003chttp://lists.ensembl.org/mailman/listinfo/dev\u003e.",""," Questions may also be sent to the Ensembl help desk at"," \u003chttp://www.ensembl.org/Help/Contact\u003e.","","=cut","","=head1 NAME","","INSTALL.pl - a script to install required code and data for VEP","","=cut","","use strict;","use FindBin qw($RealBin);","use lib $RealBin.'/modules';","use Getopt::Long;","use File::Path qw(mkpath rmtree);","use File::Copy;","use File::Basename;","use Net::FTP;","use Cwd;","use Scalar::Util qw(looks_like_number);","use Bio::EnsEMBL::VEP::Utils qw(get_version_data get_version_string);","","our ("," $DEST_DIR,"," $ENS_CVS_ROOT,"," $API_VERSION,"," $DATA_VERSION,"," $ASSEMBLY,"," $ENS_GIT_ROOT,"," $BIOPERL_URL,"," $CACHE_URL,"," $CACHE_URL_INDEXED,"," $CACHE_DIR,"," $NO_PLUGINS,"," $PLUGINS,"," $PLUGIN_URL,"," $PLUGINS_DIR,"," $FASTA_URL,"," $FTP_USER,"," $HELP,"," $NO_UPDATE,"," $SPECIES,"," $AUTO,"," $QUIET,"," $PREFER_BIN,"," $CONVERT,"," $TEST,"," $NO_HTSLIB,"," $LIB_DIR,"," $HTSLIB_DIR,"," $BIODBHTS_DIR,"," $REALPATH_DEST_DIR,"," $NO_TEST,"," $NO_BIOPERL,"," $ua,",""," $CAN_USE_CURL,"," $CAN_USE_LWP,"," $CAN_USE_HTTP_TINY,"," $CAN_USE_ARCHIVE,"," $CAN_USE_UNZIP,"," $CAN_USE_GZIP,"," $CAN_USE_TAR,"," $CAN_USE_DBI,"," $CAN_USE_DBD_MYSQL,",");","","","## VERSIONS OF INSTALLED SOFTWARE","## MAY BE UPDATED IF SUCCESSFULLY TESTED","########################################","our $HTSLIB_VERSION = '1.9'; # latest release as of release/98","our $BIOHTS_VERSION = '2.11'; # latest 2.X release as of release/98","our $BIOPERL_VERSION = 'release-1-6-924'; # frozen, no pressing need to update","","","## BEGIN BLOCK, CHECK WHAT MODULES ETC WE CAN USE","#################################################","","BEGIN {"," if(eval q{ use LWP::Simple qw(getstore get $ua); 1 }) {"," $CAN_USE_LWP = 1;",""," # set up a user agent's proxy (excluding github)"," $ua-\u003eenv_proxy;"," }",""," if(eval q{ use DBI; 1 }) {"," $CAN_USE_DBI = 1;"," }",""," if(eval q{ use DBD::mysql; 1 }) {"," $CAN_USE_DBD_MYSQL = 1;"," }",""," $CAN_USE_CURL = 1 if `which curl` =~ /\\/curl/;"," $CAN_USE_HTTP_TINY = 1 if eval q{ use HTTP::Tiny; 1 };"," $CAN_USE_ARCHIVE = 1 if eval q{ use Archive::Extract; 1 };"," $CAN_USE_UNZIP = 1 if `which unzip` =~ /\\/unzip/;"," $CAN_USE_GZIP = 1 if `which gzip` =~ /\\/gzip/;"," $CAN_USE_TAR = 1 if `which tar` =~ /\\/tar/;","}","","$| = 1;","","# CONFIGURE","###########","","# other global data","my @API_MODULES = ("," { name =\u003e 'ensembl', path =\u003e ' ', test_pm =\u003e 'Bio::EnsEMBL::Registry' },"," { name =\u003e 'ensembl-variation', path =\u003e 'Variation', test_pm =\u003e 'Bio::EnsEMBL::Variation::Variation' },"," { name =\u003e 'ensembl-funcgen', path =\u003e 'Funcgen', test_pm =\u003e 'Bio::EnsEMBL::Funcgen::RegulatoryFeature' },"," { name =\u003e 'ensembl-compara', path =\u003e 'Compara', test_pm =\u003e 'Bio::EnsEMBL::Compara::Homology' },"," { name =\u003e 'ensembl-io', path =\u003e 'IO,Utils', test_pm =\u003e 'Bio::EnsEMBL::IO::Parser' },",");","my $ensembl_url_tail = '/archive/';","my $archive_type = '.zip';","my $git_api_root = 'https://api.github.com/repos/Ensembl/';","my $VEP_MODULE_NAME = 'ensembl-vep';","","our (@store_species, @indexes, @files, $ftp, $dirname);","","my $config = {};","GetOptions("," $config,"," 'DESTDIR|DEST_DIR|d=s',"," 'CACHE_VERSION|e=i',"," 'ASSEMBLY|y=s',"," 'BIOPERL|BIOPERL_URL|b=s',"," 'CACHEURL|CACHE_URL|u=s',"," 'CACHEDIR|CACHE_DIR|c=s',"," 'FASTAURL|FASTA_URL|f=s',"," 'HELP|h',"," 'NO_UPDATE|n',"," 'SPECIES|s=s',"," 'NO_PLUGINS',"," 'PLUGINS|g=s',"," 'PLUGINSDIR|PLUGINS_DIR|r=s',"," 'PLUGINURL|PLUGIN_URL=s',"," 'AUTO|a=s',"," 'QUIET|q',"," 'PREFER_BIN|p',"," 'CONVERT|t',"," 'TEST',"," 'NO_HTSLIB|l',"," 'NO_TEST',"," 'NO_BIOPERL'",") or die(\"ERROR: Failed to parse arguments\");","","# Read configuration from environment variables starting with VEP_","# Priority is given to command-line arguments","sub read_config_from_environment {"," my $config = shift;",""," for my $key (keys %ENV) {"," # Look for environment variables that start with VEP_"," next unless $key =~ \"^VEP_\";",""," # Avoid setting empty strings"," my $value = $ENV{$key};"," next if $value eq \"\";"," $key =~ s/^VEP_//ig;",""," # Prioritise previous values"," $config-\u003e{$key} ||= $value;"," }"," return $config;","}","$config = read_config_from_environment($config);","","# Quick fix: this script should use $config instead of multiple global variables","$DEST_DIR ||= $config-\u003e{DESTDIR};","$DATA_VERSION ||= $config-\u003e{CACHE_VERSION};","$ASSEMBLY ||= $config-\u003e{ASSEMBLY};","$BIOPERL_URL ||= $config-\u003e{BIOPERL};","$CACHE_URL ||= $config-\u003e{CACHEURL};","$CACHE_DIR ||= $config-\u003e{CACHEDIR};","$FASTA_URL ||= $config-\u003e{FASTAURL};","$HELP ||= $config-\u003e{HELP};","$NO_UPDATE ||= $config-\u003e{NO_UPDATE};","$SPECIES ||= $config-\u003e{SPECIES};","$NO_PLUGINS ||= $config-\u003e{NO_PLUGINS};","$PLUGINS ||= $config-\u003e{PLUGINS};","$PLUGINS_DIR ||= $config-\u003e{PLUGINSDIR};","$PLUGIN_URL ||= $config-\u003e{PLUGINURL};","$AUTO ||= $config-\u003e{AUTO};","$QUIET ||= $config-\u003e{QUIET};","$PREFER_BIN ||= $config-\u003e{PREFER_BIN};","$CONVERT ||= $config-\u003e{CONVERT};","$TEST ||= $config-\u003e{TEST};","$NO_HTSLIB ||= $config-\u003e{NO_HTSLIB};","$NO_TEST ||= $config-\u003e{NO_TEST};","$NO_BIOPERL ||= $config-\u003e{NO_BIOPERL};","","# load version data","our $CURRENT_VERSION_DATA = get_version_data($RealBin.'/.version');","our $VERSION = $CURRENT_VERSION_DATA-\u003e{$VEP_MODULE_NAME}-\u003e{release};","$VERSION =~ s/release\\///;","","if($HELP) {"," usage();"," exit(0);","}","","# check user has DBI and DBD::mysql","die("," \"ERROR: DBI module not found. VEP requires the DBI perl module to function\\n\\n\"."," \"http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements\\n\"",") unless $CAN_USE_DBI;","","warn("," \"WARNING: DBD::mysql module not found. VEP can only run in offline (--offline) mode without DBD::mysql installed\\n\\n\"."," \"http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements\\n\"",") unless $CAN_USE_DBD_MYSQL;","","","my $default_dir_used = check_default_dir();","","$LIB_DIR = $DEST_DIR;","$HTSLIB_DIR = $LIB_DIR.'/htslib';","$BIODBHTS_DIR = $LIB_DIR.'/biodbhts';","$REALPATH_DEST_DIR .= Cwd::realpath($DEST_DIR).'/Bio';","$DEST_DIR .= '/Bio';","$dirname = dirname(__FILE__) || '.';","","$ENS_GIT_ROOT ||= 'https://github.com/Ensembl/';","$BIOPERL_URL ||= \"https://github.com/bioperl/bioperl-live/archive/$BIOPERL_VERSION.zip\";","$API_VERSION ||= $CURRENT_VERSION_DATA-\u003e{$VEP_MODULE_NAME}-\u003e{release};","$DATA_VERSION ||= $API_VERSION;","$CACHE_DIR ||= $ENV{HOME} ? $ENV{HOME}.'/.vep' : 'cache';","$PLUGINS_DIR ||= $CACHE_DIR.'/Plugins';","$FTP_USER ||= 'anonymous';","","## Set the indexed cache url if it's been overwritten by the user","$CACHE_URL_INDEXED = $CACHE_URL;","","$CACHE_URL ||= \"https://ftp.ensembl.org/pub/release-$DATA_VERSION/variation/vep\";","$CACHE_URL_INDEXED ||= \"https://ftp.ensembl.org/pub/release-$DATA_VERSION/variation/indexed_vep_cache\";","$FASTA_URL ||= \"https://ftp.ensembl.org/pub/release-$DATA_VERSION/fasta/\";","$PLUGIN_URL ||= 'https://raw.githubusercontent.com/Ensembl/VEP_plugins';","","# using PREFER_BIN can save memory when extracting archives","$PREFER_BIN = 0 unless defined($PREFER_BIN);","$Archive::Extract::PREFER_BIN = $PREFER_BIN == 0 ? 0 : 1;","","$QUIET = 0 unless $AUTO;","","# updates to ensembl-vep available?","update() unless $NO_UPDATE;","","# auto?","if($AUTO) {",""," # check"," die(\"ERROR: Failed to parse AUTO string - must contain any of a (API), l (FAIDX/htslib), c (cache), f (FASTA), p (plugins)\\n\") unless $AUTO =~ /^[alcfp]+$/i;",""," # require species"," if($AUTO =~ /[cf]/i) {"," die(\"ERROR: No species specified\\n\") unless $SPECIES;"," $SPECIES = [split /\\,/, $SPECIES];"," }",""," # require plugin list"," if($AUTO =~ /p/i) {"," die(\"ERROR: No plugins specified\\n\") unless $PLUGINS;"," $PLUGINS = [split /\\,/, $PLUGINS];"," }",""," # run subs"," if($AUTO =~ /l/ \u0026\u0026 $AUTO !~ /a/) {"," my $curdir = getcwd;"," chdir $curdir;"," install_biodbhts();"," chdir $curdir;",""," # remove Bio dir if empty"," opendir DIR, $DEST_DIR;"," my @files = grep {!/^\\./} readdir DIR;"," closedir DIR;",""," if(scalar @files \u003c= 1) {"," rmtree($DEST_DIR.'/'.$files[0]);"," rmtree($DEST_DIR);"," }"," }",""," api() if $AUTO =~ /a/;"," cache() if $AUTO =~ /c/;"," fasta() if $AUTO =~ /f/;"," plugins() if $AUTO =~ /p/;","}","","else {"," my $api_msg = "," \" - Install v$API_VERSION of the Ensembl API for use by the VEP. \" ."," \"It will not affect any existing installations of the Ensembl API that you may have.\\n\";",""," print \"Hello! This installer will help you set up VEP v$API_VERSION, including:\\n\" ."," ($NO_UPDATE ? \"\" : $api_msg) ."," \" - Download and install cache files from Ensembl's FTP server.\\n\" ."," \" - Download FASTA files from Ensembl's FTP server.\\n\" ."," ($NO_PLUGINS ? \"\" : \" - Download VEP plugins.\\n\") . \"\\n\""," unless $QUIET;",""," # run subs"," api() if check_api();"," cache();"," fasta();"," plugins() unless $NO_PLUGINS;","}","","","# clean up","if(-d \"$CACHE_DIR/tmp\" \u0026\u0026 !$TEST) {"," rmtree(\"$CACHE_DIR/tmp\") or die \"ERROR: Could not delete directory $CACHE_DIR/tmp\\n\";","}","","print \"\\nAll done\\n\" unless $QUIET;","","","##########################################################################","##########################################################################","##########################################################################","","","# UPDATE","########","sub update() {",""," my $module = $VEP_MODULE_NAME;",""," # check for major version update"," my $repo_file = \"$RealBin/$$.repo_file\";"," download_to_file("," \"$git_api_root$module\","," $repo_file"," );",""," my $default_branch;"," open IN, $repo_file;"," while(\u003cIN\u003e) {"," if(/default_branch.+\\:.+\\\"(.+?)\\\"/) {"," $default_branch = $1;"," last;"," }"," }"," close IN;",""," unlink($repo_file);",""," unless($default_branch) {"," print \"WARNING: Unable to carry out version check for '$module'\\n\" unless $QUIET;"," return;"," }",""," my $default_branch_number = $default_branch;"," $default_branch_number =~ s/release\\/// if $default_branch_number;",""," my $current_branch = $CURRENT_VERSION_DATA-\u003e{'ensembl-vep'}-\u003e{release};",""," my $message;",""," # don't have latest"," if($current_branch \u003c $default_branch_number) {"," $message = "," \"Version check reports a newer release of '$module' is available \"."," \"(installed: $current_branch, available: $default_branch_number)\\n\";"," }",""," # do have latest, but there might be updates"," elsif($current_branch == $default_branch_number) {"," my $git_sub = get_vep_sub_version($current_branch);"," my $have_sub = $CURRENT_VERSION_DATA-\u003e{$module}-\u003e{sub};",""," $message = sprintf("," \"Version check reports there are post-release updates available of %s (installed: %s.%.7s, available: %s.%.7s)\\n\","," $module,"," $current_branch, $have_sub,"," $current_branch, $git_sub"," ) unless $git_sub eq $have_sub;"," }",""," if($message) {"," print \"\\n$message\\n\";",""," # user has git, suggest they use that instead"," if(`which git` \u0026\u0026 -d $RealBin.'/.git') {"," print \"We recommend using git to update '$module', by exiting this installer and running:\\n\\n\";"," print \"\\tgit pull\\n\";"," print \"\\tgit checkout $default_branch\\n\" if $current_branch ne $default_branch_number;"," }"," else {"," print \"You should exit this installer and re-download '$module' if you wish to update\\n\";"," }",""," print \"\\nDo you wish to exit so you can get updates (y) or continue (n): \";",""," my $ok = \u003c\u003e;",""," if($ok !~ /^n/i) {"," print \"OK, bye!\\n\";"," print \"\\nNB: Remember to re-run INSTALL.pl after updating to check for API updates\\n\";"," exit(0);"," }"," }"," else {"," return;"," }","}","","","# CHECKS DIR SETUP AND PATHS ETC","################################","","sub is_url {"," my $url = shift;"," return $url =~ /^(http|ftp)/i;","}","","sub check_default_dir {"," my $this_os = $^O;"," my $default_dir_used;"," # check if $DEST_DIR is default"," if(defined($DEST_DIR)) {"," print \"Using non-default API installation directory $DEST_DIR.\\n\";"," print \"Please note this just specifies the location for downloaded API files. The vep script will remain in its current location where ensembl-vep was unzipped.\\n\";"," if(!defined($AUTO)){"," print \"Have you \\n\";"," print \"1. added $DEST_DIR to your PERL5LIB environment variable?\\n\";"," print \"2. added $DEST_DIR/htslib to your PATH environment variable?\\n\";"," if( $this_os eq 'darwin' \u0026\u0026 !$NO_HTSLIB) {"," print \"3. added $DEST_DIR/htslib to your DYLD_LIBRARY_PATH environment variable?\\n\";"," }"," print \"(y/n): \";",""," my $ok = \u003c\u003e;"," if($ok !~ /^y/i) {"," print \"Exiting. Please \\n\";"," print \"1. add $DEST_DIR to your PERL5LIB environment variable\\n\";"," print \"2. add $DEST_DIR/htslib to your PATH environment variable\\n\";"," if( $this_os eq 'darwin' \u0026\u0026 !$NO_HTSLIB) {"," print \"3. add $DEST_DIR/htslib to your DYLD_LIBRARY_PATH environment variable\\n\";"," }"," exit(0);"," }"," }"," else {"," print \"\\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\\n\\n\";"," print \"PLEASE REMEMBER TO \\n\";"," print \"1. add $DEST_DIR to your PERL5LIB environment variable\\n\";"," print \"2. add $DEST_DIR/htslib to your PATH environment variable\\n\";"," if( $this_os eq 'darwin' \u0026\u0026 !$NO_HTSLIB) {"," print \"3. add $DEST_DIR/htslib to your DYLD_LIBRARY_PATH environment variable\\n\";"," print \"\\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\\n\";"," }"," }"," if( ! -d $DEST_DIR ) {"," mkdir $DEST_DIR || die \"Could not make destination directory $DEST_DIR\""," }"," $default_dir_used = 0;"," }",""," else {"," $DEST_DIR ||= '.';"," $default_dir_used = 1;"," my $current_dir = cwd();",""," if( !$NO_HTSLIB \u0026\u0026 $this_os eq 'darwin' ) {"," print \"Installation on OSX requires that you set up some paths before running this installer.\\n\";"," if(!defined($AUTO)){"," print \"Have you \\n\";"," print \"1. added $current_dir/htslib to your DYLD_LIBRARY_PATH environment variable?\\n\";"," print \"(y/n): \";"," my $ok = \u003c\u003e;"," if($ok !~ /^y/i) {"," print \"Exiting. Please \\n\";"," print \"1. add $current_dir/htslib to your DYLD_LIBRARY_PATH environment variable\\n\";"," exit(0);"," }"," }"," else{"," print \"\\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\\n\";"," #print \"\\nPLEASE REMEMBER TO ADD $current_dir/htslib TO YOUR DYLD_LIBRARY_PATH ENVIRONMENT VARIABLE\\n\";"," print \"\\nPLEASE REMEMBER TO \\n\";"," print \"1. add $current_dir/htslib to your DYLD_LIBRARY_PATH environment variable\\n\";"," print \"\\n%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\\n\";"," }"," }"," }",""," return $default_dir_used;","}","","","# API","#####","sub api() {"," setup_dirs();"," my $curdir = getcwd;"," unless($NO_BIOPERL) {"," bioperl();"," } ",""," # htslib needs to find bioperl to pass tests"," $ENV{PERL5LIB} = $ENV{PERL5LIB} ? $ENV{PERL5LIB}.':'.$DEST_DIR : $DEST_DIR;",""," unless($NO_HTSLIB) {"," chdir $curdir;"," install_biodbhts();"," }",""," chdir $curdir;"," install_api();"," test() unless $NO_TEST;","}","","","# CHECK EXISTING","################","sub check_api() {"," return 0 if $NO_UPDATE;"," print \"Checking for installed versions of the Ensembl API...\" unless $QUIET;",""," my $has_api = {};"," my $updates = {};"," my $core_version;"," my @unknown_versions = ();",""," foreach my $module_hash(@API_MODULES) {",""," my $module = $module_hash-\u003e{name};"," my $test_pm = $module_hash-\u003e{test_pm};",""," eval \"require $test_pm\";"," $has_api-\u003e{$module} = $@ ? 0 : 1;"," "," if($has_api-\u003e{$module}) {"," my $have_sub = $CURRENT_VERSION_DATA-\u003e{$module} ? ($CURRENT_VERSION_DATA-\u003e{$module}-\u003e{sub} || '') : '';"," my $git_sub = get_module_sub_version($module);",""," if($have_sub) {"," $updates-\u003e{$module} = [$have_sub, $git_sub] if $have_sub ne $git_sub;"," }"," else {"," push @unknown_versions, $module;"," }",""," if($module eq 'ensembl') {"," $core_version = Bio::EnsEMBL::Registry-\u003esoftware_version;"," }"," }"," }",""," print \"done\\n\";",""," my $total = 0;"," $total += $_ for values %$has_api;",""," my $message;",""," if($total == scalar @API_MODULES) {",""," if(defined($core_version)) {"," if(!looks_like_number($API_VERSION)) {"," $message = \"Your reported version ($API_VERSION) is a non-standard release number\";"," }"," elsif($core_version == $API_VERSION) {",""," if(scalar keys %$updates) {"," $message ="," \"There are updates available for these modules:\\n \"."," join("," \"\\n \","," map {"," sprintf("," \"%-20s : installed = %.7s, available = %.7s\","," $_, $updates-\u003e{$_}-\u003e[0], $updates-\u003e{$_}-\u003e[1]"," )"," } keys %$updates"," );"," }"," else {"," $message = \"It looks like you already have v$API_VERSION of the API installed.\\n\";",""," if(@unknown_versions) {"," $message .="," \"No version information was available for the following modules:\\n\"."," join(\"\\n\", map {\" - \".$_} @unknown_versions)."," \"\\nUpdates may be available but you will need to perform these manually.\";"," }"," else {"," $message .= \"You shouldn't need to install the API\";"," }"," }"," }",""," elsif($core_version \u003e $API_VERSION) {"," $message = \"It looks like this installer is for an older distribution ($API_VERSION) of the API than you already have ($core_version)\";"," }",""," else {"," $message = \"It looks like you have an older version ($core_version) of the API installed.\\nThis installer will install a limited set of the API v$API_VERSION for use by the VEP only\";"," }"," }",""," else {"," $message = \"It looks like you have an unidentified version of the API installed.\\nThis installer will install a limited set of the API v$API_VERSION for use by the VEP only\""," }"," }",""," elsif($total \u003e 0) {"," $message = \"It looks like you already have the following API modules installed:\\n\\n\".(join \"\\n\", grep {$has_api-\u003e{$_}} keys %$has_api).\"\\n\\nEnsembl VEP requires the ensembl, ensembl-io, ensembl-variation, ensembl-compara and ensembl-funcgen modules\";"," }",""," if($AUTO =~ /a/ || !defined($message)) {"," return 1;"," }"," else {"," print $message unless $QUIET;",""," print \"\\n\\nSkip to the next step (n) to install cache files\\n\\nDo you want to continue installing the API (y/n)? \";"," my $ok = \u003c\u003e;",""," if($ok !~ /^y/i) {"," print \" - skipping API installation\\n\" unless $QUIET;"," return 0;"," }"," else {"," return 1;"," }"," }","}","","","# SETUP","#######","sub setup_dirs() {",""," print \"\\nSetting up directories\\n\" unless $QUIET;",""," # check if install dir exists"," if(-e $DEST_DIR) {"," my $ok;",""," if($AUTO) {"," $ok = 'y';"," }"," else {"," print \"Destination directory $DEST_DIR already exists.\\nDo you want to overwrite it (if updating VEP this is probably OK) (y/n)? \";",""," $ok = \u003c\u003e;"," }",""," if($ok !~ /^y/i) {"," print \"Exiting\\n\";"," exit(0);"," }",""," else {"," unless($default_dir_used || $AUTO) {"," print \"WARNING: You are using a non-default install directory.\\nPressing \\\"y\\\" again will remove $DEST_DIR and its contents!!!\\nAre you really, really sure (y/n)? \";"," $ok = \u003c\u003e;",""," if($ok !~ /^y/i) {"," print \"Exiting\\n\";"," exit(0);"," }"," }",""," # try to delete the existing dir"," rmtree($DEST_DIR) or die \"ERROR: Could not delete directory $DEST_DIR\\n\";"," }"," }",""," mkdir($DEST_DIR) or die \"ERROR: Could not make directory $DEST_DIR\\n\";"," mkdir($DEST_DIR.'/tmp') or die \"ERROR: Could not make directory $DEST_DIR/tmp\\n\";","}","","","# INSTALL API","#############","sub install_api() {",""," print \"\\nDownloading required Ensembl API files\\n\" unless $QUIET;",""," my $release_url_string = looks_like_number($API_VERSION) ? 'release/'.$API_VERSION : $API_VERSION;"," my $release_path_string = looks_like_number($API_VERSION) ? 'release-'.$API_VERSION : $API_VERSION;",""," foreach my $module_hash(@API_MODULES) {"," my $module = $module_hash-\u003e{name};",""," # do we need to update this?"," my $have_sub = $CURRENT_VERSION_DATA-\u003e{$module} ? ($CURRENT_VERSION_DATA-\u003e{$module}-\u003e{sub} || '') : '';",""," my $url = $ENS_GIT_ROOT.$module.$ensembl_url_tail.$release_url_string.$archive_type;",""," print \" - fetching $module\\n\" unless $QUIET;"," my $target_file = $DEST_DIR.'/tmp/'.$module.$archive_type;"," mkdir($DEST_DIR.'/tmp/') unless -d $DEST_DIR.'/tmp/';"," download_to_file($url, $target_file) unless -e $target_file;",""," print \" - unpacking $target_file\\n\" unless $QUIET;"," unpack_arch(\"$DEST_DIR/tmp/$module$archive_type\", \"$DEST_DIR/tmp/\");",""," print \" - moving files\\n\" unless $QUIET;"," foreach my $module_path (split(',',$module_hash-\u003e{path})) {"," my $module_dir_suffix = $module_path eq ' ' ? '' : '/'.$module_path;"," my $module_dir_from = \"$DEST_DIR/tmp/$module\\-$release_path_string/modules/Bio/EnsEMBL$module_dir_suffix\";"," my $module_dir_to = \"$DEST_DIR/EnsEMBL$module_dir_suffix\";",""," # If the target directory already exist, we can't overwrite it."," if (-d $module_dir_to) {"," # One solution is to move the content of the directory instead."," # However we need to loop over the files/directories within the module directory because the 'move()' method doesn't allow wildcards."," opendir DH, $module_dir_from;"," while(my $file_or_dir = readdir DH) {"," next if ($file_or_dir =~ /^\\.+$/);"," move(\"$module_dir_from/$file_or_dir\", \"$module_dir_to/$file_or_dir\") or die \"ERROR: Could not move '$module_dir_from/$file_or_dir'\\n\".$!;"," }"," closedir DH;"," }"," else {"," move($module_dir_from, $module_dir_to) or die \"ERROR: Could not move the directory '$module_dir_from'\\n\".$!;"," }"," }",""," # now get latest commit from github API"," print \" - getting version information\\n\" unless $QUIET;"," my $git_sub = get_module_sub_version($module);",""," mkdir(\"$RealBin/.version/\") unless -d \"$RealBin/.version/\";"," open OUT, \"\u003e$RealBin/.version/$module\" or die $!;"," print OUT \"release $API_VERSION\\nsub $git_sub\\n\";"," close OUT;",""," rmtree(\"$DEST_DIR/tmp/$module\\-$release_path_string\") or die \"ERROR: Failed to remove directory: $!\\n\";"," }","}","","sub get_module_sub_version {"," my $module = shift;",""," my $sub_file = \"$RealBin/$$\\.$module.sub\";"," my $release_url_string = looks_like_number($API_VERSION) ? 'release/'.$API_VERSION : $API_VERSION;",""," download_to_file("," \"$git_api_root$module/commits?sha=$release_url_string\","," $sub_file"," );",""," open IN, $sub_file or die $!;"," my $sub;"," while(\u003cIN\u003e) {"," if(/\\\"sha\\\": \\\"(.+?)\\\"/) {"," $sub = $1;"," last;"," }"," }"," close IN;",""," unlink($sub_file);",""," return $sub;","}","","sub get_vep_sub_version {"," my $release = shift || $API_VERSION;",""," my $sub_file = \"$RealBin/$$\\.$VEP_MODULE_NAME.sub\";"," my $release_url_string = looks_like_number($release) ? 'release/'.$release : $release;",""," download_to_file("," sprintf("," 'https://raw.githubusercontent.com/Ensembl/%s/%s/modules/Bio/EnsEMBL/VEP/Constants.pm',"," $VEP_MODULE_NAME,"," $release_url_string"," ),"," $sub_file"," );",""," open IN, $sub_file or die $!;"," my $sub;"," while(\u003cIN\u003e) {"," if(/VEP_SUB_VERSION \\= (.+)\\;/) {"," $sub = $1;"," last;"," }"," }"," close IN;",""," unlink($sub_file);",""," return $sub;","}","","# HTSLIB download/make","######################","sub install_htslib() {",""," #actually decided to follow Bio::DB::Sam template"," # STEP 0: various dependencies"," my $git = `which git`;"," $git or die \u003c\u003cEND;"," 'git' command not in path. Please install git and try again."," (or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)",""," On Debian/Ubuntu systems you can do this with the command:",""," apt-get install git","END","",""," `which cc` or die \u003c\u003cEND;"," 'cc' command not in path. Please install it and try again."," (or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)",""," On Debian/Ubuntu systems you can do this with the command:",""," apt-get install build-essential","END",""," `which make` or die \u003c\u003cEND;"," 'make' command not in path. Please install it and try again."," (or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)",""," On Debian/Ubuntu systems you can do this with the command:",""," apt-get install build-essential","END"," "," # List the required libraries with their packages"," my %libs = ( "," 'zlib.h' =\u003e 'zlib1g-dev', "," 'lzma.h' =\u003e 'liblzma-dev', "," 'bzlib.h' =\u003e 'libbz2-dev'"," );",""," my $msg = '';"," my $this_os = $^O;",""," if ($this_os ne 'darwin' ) {"," "," my $default_msg = qq{%s library header(s) not found in /usr/include. Please install it and try again.","(or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)","","On Debian/Ubuntu systems you can do this with the command:","","apt-get install %s};"," my @missing_header = ();"," my @missing_library = (); "," # Loop over the required libraries"," foreach my $lib (sort(keys(%libs))) {"," unless(-e '/usr/include/'.$lib){"," push(@missing_header, $lib);","\tpush(@missing_library, $libs{$lib});"," }"," }"," my $header_string = join( ', ', @missing_header);"," my $install_string = join( ' ', @missing_library);"," die(sprintf($default_msg, $header_string, $install_string). \"\\n\\n\") if($header_string ne '');"," }"," "," # STEP 1: Create a clean directory for building"," my $htslib_install_dir = $LIB_DIR;"," my $curdir = getcwd;"," chdir $htslib_install_dir;"," my $actualdir = getcwd;",""," # STEP 2: Check out HTSLIB / or make this a download?"," print(\" - checking out HTSLib\\n\");"," system \"git clone -b $HTSLIB_VERSION https://github.com/samtools/htslib.git\";"," -d './htslib' or die \"git clone seems to have failed. Could not find $htslib_install_dir/htslib directory\";"," chdir './htslib';",""," # Step 3: Build libhts.a"," print(\" - building HTSLIB in $htslib_install_dir/htslib\\n\");"," print( \"In \".getcwd.\"\\n\" );"," # patch makefile"," rename 'Makefile','Makefile.orig' or die \"Couldn't rename Makefile to Makefile.orig: $!\";"," open my $in, '\u003c','Makefile.orig' or die \"Couldn't open Makefile for reading: $!\";"," open my $out,'\u003e','Makefile.new' or die \"Couldn't open Makefile.new for writing: $!\";",""," while (\u003c$in\u003e) {"," chomp;"," if (/^CFLAGS/ \u0026\u0026 !/-fPIC/) {"," s/#.+//; # get rid of comments"," $_ .= \" -fPIC -Wno-unused -Wno-unused-result\";"," }"," }"," continue {"," print $out $_,\"\\n\";"," }",""," close $in;"," close $out;"," rename 'Makefile.new','Makefile' or die \"Couldn't rename Makefile.new to Makefile: $!\";"," system \"make\";"," -e 'libhts.a' or die \"Compile didn't complete. No libhts.a library file found\";",""," chdir $curdir;"," my $retval = Cwd::realpath(\"$htslib_install_dir/htslib\") ;","}","","","# INSTALL Bio::DB::HTS","######################","sub install_biodbhts() {",""," print \"Attempting to install Bio::DB::HTS and htslib.\\n\\n\u003e\u003e\u003e If this fails, try re-running with --NO_HTSLIB\\n\\n\";",""," my $htslib_location = install_htslib();"," rmtree( $DEST_DIR.'/tmp' );",""," #Now install Bio::DB::HTS proper"," my $biodbhts_github_url = \"https://github.com/Ensembl/Bio-DB-HTS\";"," my $biodbhts_zip_github_url = \"$biodbhts_github_url/archive/$BIOHTS_VERSION.zip\";"," my $biodbhts_zip_download_file = $DEST_DIR.'/tmp/biodbhts.zip';",""," mkdir $DEST_DIR unless -d $DEST_DIR;"," mkdir $DEST_DIR.'/tmp';"," download_to_file($biodbhts_zip_github_url, $biodbhts_zip_download_file);"," print \" - unpacking $biodbhts_zip_download_file to $DEST_DIR/tmp/\\n\" unless $QUIET;"," unpack_arch($biodbhts_zip_download_file, \"$DEST_DIR/tmp/\");",""," my $tmp_name = -d \"$DEST_DIR/tmp/Bio-HTS-$BIOHTS_VERSION\" ? \"Bio-HTS-$BIOHTS_VERSION\" : \"Bio-DB-HTS-$BIOHTS_VERSION\";",""," print \"$DEST_DIR/tmp/$tmp_name - moving files to $BIODBHTS_DIR\\n\" unless $QUIET;"," rmtree($BIODBHTS_DIR);"," move(\"$DEST_DIR/tmp/$tmp_name\", $BIODBHTS_DIR) or die \"ERROR: Could not move directory\\n\".$!;",""," print( \" - making Bio::DB:HTS\\n\" );"," # patch makefile"," chdir $BIODBHTS_DIR;"," system \"perl Build.PL --htslib $htslib_location\";"," system \"./Build\";"," chdir \".\";",""," #move the library"," my $pdir = getcwd;",""," #Perl modules to go alongside the API"," dircopy(\"lib/Bio\",$REALPATH_DEST_DIR);",""," #The shared object XS library"," if( -e \"blib/arch/auto/Bio/DB/HTS/HTS.so\" ) {"," copy( \"blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so\", \"..\")"," or die \"ERROR: Could not copy shared Faidx.so library:$!\\n\";"," copy( \"blib/arch/auto/Bio/DB/HTS/HTS.so\", \"..\")"," or die \"ERROR: Could not copy shared HTS.so library:$!\\n\";"," }"," elsif( -e \"blib/arch/auto/Bio/DB/HTS/HTS.bundle\" ) {"," copy( \"blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bundle\", \"..\")"," or die \"ERROR: Could not copy shared Faidx.bundle library:$!\\n\";"," copy( \"blib/arch/auto/Bio/DB/HTS/HTS.bundle\", \"..\")"," or die \"ERROR: Could not copy shared HTS.bundle library:$!\\n\";"," }"," else {"," die \"ERROR: Shared Bio::DB:HTS library not found\\n\";"," }",""," chdir $pdir;","}","","sub dircopy {"," my ($from, $to) = @_;",""," opendir FROM, $from;",""," foreach my $file(grep {!/^\\.\\.?/} readdir FROM) {",""," # dir?"," if(-d \"$from/$file\") {"," mkdir(\"$to/$file\") unless -d \"$to/$file\";"," dircopy(\"$from/$file\", \"$to/$file\");"," }"," else {"," copy(\"$from/$file\", \"$to/$file\");"," }"," }",""," closedir FROM;","}","","","# INSTALL BIOPERL","#################","sub bioperl() {",""," # now get BioPerl"," print \" - fetching BioPerl\\n\" unless $QUIET;",""," my $bioperl_file = (split /\\//, $BIOPERL_URL)[-1];",""," my $target_file = $DEST_DIR.'/tmp/'.$bioperl_file;",""," download_to_file($BIOPERL_URL, $target_file);",""," print \" - unpacking $target_file\\n\" unless $QUIET;"," unpack_arch(\"$DEST_DIR/tmp/$bioperl_file\", \"$DEST_DIR/tmp/\");",""," print \" - moving files\\n\" unless $QUIET;",""," my $bioperl_dir;",""," if($BIOPERL_URL =~ /github/) {"," $bioperl_file =~ s/\\.zip//;"," $bioperl_dir = \"bioperl-live-\".$bioperl_file;"," }"," else {"," $bioperl_file =~ /(bioperl.+?)\\.tar\\.gz/i;"," $bioperl_dir = $1;"," }",""," opendir BIO, \"$DEST_DIR/tmp/$bioperl_dir/Bio/\";"," move(\"$DEST_DIR/tmp/$bioperl_dir/Bio/$_\", \"$DEST_DIR/$_\") for readdir BIO;"," closedir BIO;",""," rmtree(\"$DEST_DIR/tmp\") or die \"ERROR: Failed to remove directory $DEST_DIR/tmp\\n\";","}","","","# TEST","######","sub test() {",""," print \"\\nTesting VEP installation\\n\" unless $QUIET;",""," eval q{use Test::Harness; use Test::Exception; };"," if(!$@) {"," opendir TEST, \"$dirname\\/t\";"," my @test_files = map {\"$dirname\\/t\\/\".$_} grep {!/^\\./ \u0026\u0026 /\\.t$/} readdir TEST;"," closedir TEST;",""," # haplo.pl tests require Set::IntervalTree which is not installed here"," eval q{use Set::IntervalTree};"," @test_files = grep {!/Haplo/} @test_files if $@;",""," print \"Warning: Tests failed, VEP may not run correctly\\n\" unless runtests(@test_files);"," }"," else {"," my $test_vep = `perl -I $DEST_DIR $dirname/vep --help 2\u003e\u00261`;",""," $test_vep =~ /ENSEMBL VARIANT EFFECT PREDICTOR/ or die \"ERROR: Testing VEP script failed with the following error\\n$test_vep\\n\";"," }",""," print \" - OK!\\n\" unless $QUIET;","}","","","# CACHE FILES","#############","","sub format_file_size {"," # Format $size (in bytes) based on most adequate unit, e.g.:"," # 0 =\u003e 0 bytes"," # 421 =\u003e 421 bytes"," # 1000 =\u003e 1 KB"," # 432340000 =\u003e 432 MB"," # 62340002001 =\u003e 62 GB"," # 3126340002001 =\u003e 3 TB"," "," my $size = shift;"," # Units sorted from the biggest to smallest order of magnitude"," my @units = ( 'TB', 'GB', 'MB', 'KB', 'bytes' );"," "," while (@units) {"," my $unit = shift @units;"," # Calculate order of magnitude based on length of @units"," my $factor = 10 ** ( 3 * scalar @units );"," return int($size / $factor) . \" \" . $unit if $size \u003e= $factor || $unit eq \"bytes\";"," }","}","","sub cache() {",""," my $ok;",""," if($AUTO) {"," $ok = $AUTO =~ /c/i ? 'y' : 'n';"," }"," else {"," print \"\\nThe VEP can either connect to remote or local databases, or use local cache files.\\nUsing local cache files is the fastest and most efficient way to run the VEP\\n\" unless $QUIET;"," print \"Cache files will be stored in $CACHE_DIR\\n\" unless $QUIET;",""," print \"Do you want to install any cache files (y/n)? \";",""," $ok = \u003c\u003e;"," }",""," if($ok !~ /^y/i) {"," print \"Skipping cache installation\\n\" unless $QUIET;"," return;"," }",""," # check cache dir exists"," if(!(-e $CACHE_DIR)) {"," if(!$AUTO) {"," print \"Cache directory $CACHE_DIR does not exists - do you want to create it (y/n)? \";",""," my $ok = \u003c\u003e;",""," if($ok !~ /^y/i) {"," print \"Exiting\\n\";"," exit(0);"," }"," }",""," mkdir($CACHE_DIR) or die \"ERROR: Could not create directory $CACHE_DIR\\n\";"," }",""," mkdir($CACHE_DIR.'/tmp') unless -e $CACHE_DIR.'/tmp';",""," # get list of species"," print \" - getting list of available cache files\\n\" unless $QUIET;",""," my $bgzip = `which bgzip`;"," chomp($bgzip);"," $bgzip ||= \"$HTSLIB_DIR/bgzip\";",""," my $tabix = `which tabix`;"," chomp($tabix);"," $tabix ||= \"$HTSLIB_DIR/tabix\";"," "," my $URL_TO_USE = (-e $tabix) ? $CACHE_URL_INDEXED : $CACHE_URL;",""," if(is_url($URL_TO_USE)) {"," $URL_TO_USE =~ m/(.*:\\/\\/)?(.+?)\\/(.+)/;"," $ftp = Net::FTP-\u003enew($2, Passive =\u003e 1) or die \"ERROR: Could not connect to FTP host $2\\n$@\\n\";"," $ftp-\u003elogin($FTP_USER) or die \"ERROR: Could not login as $FTP_USER\\n$@\\n\";"," $ftp-\u003ebinary();",""," foreach my $sub(split /\\//, $3) {"," $ftp-\u003ecwd($sub) or die \"ERROR: Could not change directory to $sub\\n$@\\n\";"," }",""," push @files, grep {$_ =~ /tar.gz/} $ftp-\u003els;"," }"," else {"," opendir DIR, $URL_TO_USE;"," @files = grep {$_ =~ /tar.gz/} readdir DIR;"," closedir DIR;"," }",""," # if we don't have a species list, we'll have to guess"," if(!scalar(@files)) {"," print \"Could not get current species list - using predefined list instead\\n\";"," print \"For more species, see http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre\\n\";",""," @files = ("," \"bos_taurus_vep_\".$DATA_VERSION.\"_UMD3.1.tar.gz\","," \"danio_rerio_vep_\".$DATA_VERSION.\"_GRCz11.tar.gz\","," \"homo_sapiens_vep_\".$DATA_VERSION.\"_GRCh37.tar.gz\","," \"homo_sapiens_vep_\".$DATA_VERSION.\"_GRCh38.tar.gz\","," \"mus_musculus_vep_\".$DATA_VERSION.\"_GRCm38.tar.gz\","," \"rattus_norvegicus_vep_\".$DATA_VERSION.\"_Rnor_6.0.tar.gz\","," );"," }"," else {"," # sort"," @files = sort {($a =~ /homo_sapiens/) \u003c=\u003e ($b =~ /homo_sapiens/) || $a cmp $b} @files;"," }",""," my $num = 0;"," my $species_list;"," my $size;"," my $total_size = 0;"," foreach my $file(@files) {"," $size = defined $ftp ? $ftp-\u003esize($file) : 0;"," $total_size += $size;"," $size = $size ? \" (\" . format_file_size($size) . \")\" : \"\";"," $species_list .= ++$num . \" : $file$size\\n\";"," }",""," if($AUTO) {"," if($SPECIES-\u003e[0] eq 'all') {"," @indexes = (1..(scalar @files));"," }",""," else {"," foreach my $sp(@$SPECIES) {"," my @matches;",""," for my $i(0..$#files) {"," if($sp =~ /refseq|merged/i) {"," push @matches, $i + 1 if $files[$i] =~ /$sp/i;"," }"," else {"," push @matches, $i + 1 if $files[$i] =~ /$sp/i \u0026\u0026 $files[$i] !~ /refseq|merged/i;"," }"," }",""," # grep assembly if supplied"," @matches = grep {$files[$_ - 1] =~ /\\_$ASSEMBLY\\./} @matches if $ASSEMBLY;",""," if(scalar @matches == 1) {"," push @indexes, @matches;"," }"," elsif(scalar @matches \u003e 1) {"," # xenopus_tropicalis_vep_76_JGI_4.2.tar.gz",""," my @assemblies = ();"," foreach my $m(@matches) {"," $files[$m-1] =~ m/\\_vep\\_$DATA_VERSION\\_(.+?)\\.tar\\.gz/;"," push @assemblies, $1 if $1;"," }",""," die(\"ERROR: Multiple assemblies found (\".join(\", \", @assemblies).\") for $sp; select one using --ASSEMBLY [name]\\n\")"," }"," }"," }",""," die(\"ERROR: No matching species found\") unless scalar @indexes;",""," # uniquify and sort"," @indexes = sort {$a \u003c=\u003e $b} keys %{{map {$_ =\u003e 1} @indexes}};"," }"," else {"," $total_size = $total_size \u003c= 0 ? \"\" :"," \" \" . format_file_size($total_size) . \" for all\";"," print \"The following species/files are available; which do you want \" ."," \"(specify multiple separated by spaces or 0 for all): \\n\"."," \"$species_list\\n Total:$total_size $num files\\n\\n? \";"," @indexes = split /\\s+/, \u003c\u003e;",""," # user wants all species found"," if(scalar @indexes == 1 \u0026\u0026 $indexes[0] == 0) {"," @indexes = 1..(scalar @files);"," }"," }",""," foreach my $file(@indexes) {"," die(\"ERROR: File number $file not valid\\n\") unless defined($file) \u0026\u0026 $file =~ /^[0-9]+$/ \u0026\u0026 defined($files[$file - 1]);",""," my $file_path = $files[$file - 1];",""," my $refseq = 0;"," my ($species, $assembly, $file_name);",""," if($file_path =~ /\\//) {"," ($species, $file_name) = (split /\\//, $file_path);"," $file_name =~ m/^(\\w+?)\\_vep\\_\\d+\\_(.+?)\\.tar\\.gz/;"," $assembly = $2;"," }"," else {"," $file_name = $file_path;"," $file_name =~ m/^(\\w+?)\\_vep\\_\\d+\\_(.+?)\\.tar\\.gz/;"," $species = $1;"," $assembly = $2;"," }",""," push @store_species, $species;",""," # check if user already has this species and version"," if(-e \"$CACHE_DIR/$species/$DATA_VERSION\\_$assembly\") {",""," my $ok;",""," print \"\\nWARNING: It looks like you already have the cache for $species $assembly (v$DATA_VERSION) installed.\\n\" unless $QUIET;",""," if($AUTO) {"," print \"\\nDelete the folder $CACHE_DIR/$species/$DATA_VERSION\\_$assembly and re-run INSTALL.pl if you want to re-install\\n\";"," }"," else {"," print \"If you continue the existing cache will be overwritten.\\nAre you sure you want to continue (y/n)? \";",""," $ok = \u003c\u003e;"," }",""," if($ok !~ /^y/i) {"," print \" - skipping $species\\n\" unless $QUIET;"," next;"," }",""," rmtree(\"$CACHE_DIR/$species/$DATA_VERSION\\_$assembly\") or die \"ERROR: Could not delete directory $CACHE_DIR/$species/$DATA_VERSION\\_$assembly\\n\";"," }",""," if($species =~ /refseq/i) {"," print \"NB: Remember to use --refseq when running the VEP with this cache!\\n\" unless $QUIET;"," }"," if($species =~ /merged/i) {"," print \"NB: Remember to use --merged when running the VEP with this cache!\\n\" unless $QUIET;"," }",""," my $target_file = \"$CACHE_DIR/tmp/$file_name\";"," if(is_url($URL_TO_USE)) {"," print \" - downloading $URL_TO_USE/$file_path\\n\" unless $QUIET;"," if(!$TEST) {"," $ftp-\u003eget($file_name, $target_file) or download_to_file(\"$URL_TO_USE/$file_path\", $target_file);",""," my $checksums = \"CHECKSUMS\";"," my $checksums_target_file = \"$CACHE_DIR/tmp/$checksums\";"," $ftp-\u003eget($checksums, $checksums_target_file) or download_to_file(\"$URL_TO_USE/$checksums\", $checksums_target_file);"," if (-e $checksums_target_file) {"," my $sum_download = `sum $target_file`;"," $sum_download =~ m/([0-9]+)(\\s+)([0-9]+)/;"," my $checksum_download = $1;"," $checksum_download =~ s/^0*//;"," my $sum_ftp = `grep $file_name $checksums_target_file`;"," $sum_ftp =~ s/^0*//;"," if ($sum_download \u0026\u0026 $sum_ftp) {"," die(\"ERROR: checksum for $target_file doesn't match checksum in CHECKSUMS file on FTP site\\n\") if ($sum_ftp !~ m/^$checksum_download\\s+/);"," }"," }"," }"," }"," else {"," print \" - copying $URL_TO_USE/$file_path\\n\" unless $QUIET;"," copy(\"$URL_TO_USE/$file_path\", $target_file) unless $TEST;"," }",""," print \" - unpacking $file_name\\n\" unless $QUIET;","",""," unpack_arch($target_file, $CACHE_DIR.'/tmp/') unless $TEST;",""," # does species dir exist?"," if(!-e \"$CACHE_DIR/$species\" \u0026\u0026 !$TEST) {"," mkdir(\"$CACHE_DIR/$species\") or die \"ERROR: Could not create directory $CACHE_DIR/$species\\n\";"," }",""," # move files"," unless($TEST) {"," opendir CACHEDIR, \"$CACHE_DIR/tmp/$species/\";"," move(\"$CACHE_DIR/tmp/$species/$_\", \"$CACHE_DIR/$species/$_\") for readdir CACHEDIR;"," closedir CACHEDIR;"," }"," "," if(((-e $bgzip \u0026\u0026 -e $tabix) || $CONVERT) \u0026\u0026 !$TEST) {"," unless($QUIET) {"," print \" - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster\\n\";"," print \" - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)\\n\";"," }"," system(\"perl $dirname/convert_cache.pl --dir $CACHE_DIR --species $species --version $DATA_VERSION\\_$assembly --bgzip $bgzip --tabix $tabix\") == 0 or print STDERR \"WARNING: Failed to run convert script\\n\";"," }"," }","}","","","# FASTA FILES","#############","sub fasta() {",""," ### SPECIAL CASE GRCh37"," if((grep {$files[$_ - 1] =~ /GRCh37/} @indexes) || (defined($ASSEMBLY) \u0026\u0026 $ASSEMBLY eq 'GRCh37')) {",""," # can't install other species at same time as the FASTA URL has to be changed"," if(grep {$files[$_ - 1] !~ /GRCh37/} @indexes) {"," die(\"ERROR: For technical reasons this installer is unable to install GRCh37 caches alongside others; please install them separately\\n\");"," }",""," # change URL to point to last e! version that had GRCh37 downloads"," elsif(is_url($FASTA_URL)) {"," print \"\\nWARNING: Changing URL for GRCh37\\n\";"," $FASTA_URL =~ s/$DATA_VERSION/75/;"," }"," }",""," my $ok;",""," if($AUTO) {"," $ok = $AUTO =~ /f/i ? 'y' : 'n';"," }"," else {"," print \"\\nThe VEP can use FASTA files to retrieve sequence data for HGVS notations and reference sequence checks.\\n\" unless $QUIET;"," print \"FASTA files will be stored in $CACHE_DIR\\n\" unless $QUIET;"," print \"Do you want to install any FASTA files (y/n)? \";",""," $ok = \u003c\u003e;"," }",""," if($ok !~ /^y/i) {"," print \"Skipping FASTA installation - Exiting\\n\";"," return;"," }",""," my @dirs = ();",""," if(is_url($FASTA_URL)) {"," $FASTA_URL =~ m/(.*:\\/\\/)?(.+?)\\/(.+)/;"," $ftp = Net::FTP-\u003enew($2, Passive =\u003e 1) or die \"ERROR: Could not connect to FTP host $2\\n$@\\n\";"," $ftp-\u003elogin($FTP_USER) or die \"ERROR: Could not login as $FTP_USER\\n$@\\n\";"," $ftp-\u003ebinary();",""," foreach my $sub(split /\\//, $3) {"," $ftp-\u003ecwd($sub) or die \"ERROR: Could not change directory to $sub\\n$@\\n\";"," }"," push @dirs, grep { !/ancestral_alleles/i } sort $ftp-\u003els;"," }"," else {"," opendir DIR, $FASTA_URL;"," @dirs = grep {-d $FASTA_URL.'/'.$_ \u0026\u0026 $_ !~ /^\\./} readdir DIR;"," closedir DIR;"," }",""," my $species_list = '';"," my $num = 1;"," foreach my $dir(@dirs) {"," $species_list .= $num++.\" : \".$dir.\"\\n\";"," }",""," my @species;"," if($AUTO) {"," if($SPECIES-\u003e[0] eq 'all') {"," @species = scalar @store_species ? @store_species : @dirs;"," }"," else {"," @species = scalar @store_species ? @store_species : @$SPECIES;"," }"," }"," else {"," print \"FASTA files for the following species are available; which do you want (can specify multiple separated by spaces, \\\"0\\\" to install for species specified for cache download): \\n$species_list\\n? \";",""," my $input = \u003c\u003e;"," my @nums = split /\\s+/, $input;",""," @species = @store_species if grep {$_ eq '0'} @nums;"," push @species, $dirs[$_ - 1] for grep {$_ \u003e 0} @nums;"," }",""," foreach my $species(@species) {",""," # remove refseq name"," my $orig_species = $species;"," $species =~ s/_refseq//;"," $species =~ s/_merged//;",""," my @files;"," my $dna_path;",""," if($ftp) {"," $ftp-\u003ecwd($species) or die \"ERROR: Could not change directory to $species\\n$@\\n\";"," $ftp-\u003ecwd('dna_index') or $ftp-\u003ecwd('dna') or die \"ERROR: Could not change directory to dna\\n$@\\n\";"," @files = $ftp-\u003els;"," $dna_path = $ftp-\u003epwd =~ /dna_index/ ? 'dna_index' : 'dna';"," }"," else {"," if(!opendir DIR, \"$FASTA_URL/$species/dna\") {"," warn \"WARNING: Could not read from directory $FASTA_URL/$species/dna\\n$@\\n\";"," next;"," }"," @files = grep {$_ !~ /^\\./} readdir DIR;"," closedir DIR;"," }",""," # remove repeat/soft-masked files"," @files = grep {!/_(s|r)m\\./} @files;",""," my ($file) = grep {/primary_assembly.fa.gz$/} @files;"," ($file) = grep {/toplevel.fa.gz$/} @files if !defined($file);",""," unless(defined($file)) {"," warn \"WARNING: No download found for $species\\n\";"," next;"," }",""," # work out assembly version from file name"," my $uc_species = ucfirst($species);"," $file =~ m/^$uc_species\\.(.+?)(\\.)?(\\d+)?\\.dna/;"," my $assembly = $1;",""," # second number could be an Ensembl release number (pre-76) or part of the assembly name"," if(defined($3)) {"," if(!grep {$3 == $_} (69..75)) {"," $assembly .= $2.$3;"," }"," }",""," die(\"ERROR: Unable to parse assembly name from $file\\n\") unless $assembly;",""," my $ex = \"$CACHE_DIR/$orig_species/$DATA_VERSION\\_$assembly/$file\";"," my $ex_unpacked = $ex;"," $ex_unpacked =~ s/\\.gz$//;"," if(-e $ex || -e $ex_unpacked) {"," print \"Looks like you already have the FASTA file for $orig_species, skipping\\n\" unless $QUIET;",""," if($ftp) {"," $ftp-\u003ecwd('../');"," $ftp-\u003ecwd('../');"," }"," next;"," }",""," # create path"," mkdir($CACHE_DIR) unless -d $CACHE_DIR || $TEST;"," mkdir(\"$CACHE_DIR/$orig_species\") unless -d \"$CACHE_DIR/$orig_species\" || $TEST;"," mkdir(\"$CACHE_DIR/$orig_species/$DATA_VERSION\\_$assembly\") unless -d \"$CACHE_DIR/$orig_species/$DATA_VERSION\\_$assembly\" || $TEST;",""," if($ftp) {"," print \" - downloading $file\\n\" unless $QUIET;"," if(!$TEST) {"," $ftp-\u003eget($file, $ex) or download_to_file(\"$FASTA_URL/$species/$dna_path/$file\", $ex);"," }"," }"," else {"," print \" - copying $file\\n\" unless $QUIET;"," copy(\"$FASTA_URL/$species/dna/$file\", $ex) unless $TEST;"," }",""," my $bgzip = `which bgzip`;"," chomp($bgzip);"," $bgzip ||= \"$HTSLIB_DIR/bgzip\";",""," eval q{ use Bio::DB::HTS::Faidx; };"," my $can_use_faidx = $@ ? 0 : 1;",""," if($can_use_faidx) {",""," if($dna_path !~ /dna_index/ \u0026\u0026 -e $bgzip \u0026\u0026 $CAN_USE_GZIP) {"," print \" - converting sequence data to bgzip format, this may take some time...\\n\" unless $QUIET;"," my $curdir = getcwd;"," my $bgzip_convert = \"gzip -dc $ex | $bgzip -c \u003e $ex\\.bgz; mv $ex\\.bgz $ex\";"," my $bgzip_result = `$bgzip_convert` unless $TEST;",""," if( $? != 0 ) {"," die \"FASTA gzip to bgzip conversion failed: $bgzip_result\\n\" unless $TEST;"," }"," else {"," print \" - conversion successful\\n\";"," }"," }",""," my $got_indexes = 0;"," foreach my $index_file(grep {/$file\\..+/} @files) {"," if(!$TEST) {"," $index_file =~ /$file(\\..+)/;"," print \" - downloading $index_file\\n\" unless $QUIET;"," $ftp-\u003eget($index_file, $ex.$1) or download_to_file(\"$FASTA_URL/$species/$dna_path/$index_file\", $ex.$1);"," $got_indexes++;"," }"," }",""," unless($got_indexes == 2) {"," print \" - indexing FASTA file\\n\" unless $QUIET;"," Bio::DB::HTS::Faidx-\u003enew($ex) unless $TEST;"," print \" - indexing OK\\n\" unless $QUIET;"," }",""," print \"\\nThe FASTA file should be automatically detected by the VEP when using --cache or --offline.\\nIf it is not, use \\\"--fasta $ex\\\"\\n\\n\" unless $QUIET;"," }",""," elsif($NO_HTSLIB) {"," print \" - extracting data\\n\" unless $QUIET;"," unpack_arch($ex, \"$CACHE_DIR/$orig_species/$DATA_VERSION\\_$assembly/\") unless $TEST;",""," print \" - attempting to index\\n\" unless $QUIET;"," eval q{"," use Bio::DB::Fasta;"," };"," if($@) {"," print \"Indexing failed - VEP will attempt to index the file the first time you use it\\n\" unless $QUIET;"," }"," else {"," print \" - indexing FASTA file\\n\" unless $QUIET;"," Bio::DB::Fasta-\u003enew($ex_unpacked) unless $TEST;"," print \" - indexing OK\\n\" unless $QUIET;"," }",""," print \"\\nThe FASTA file should be automatically detected by the VEP when using --cache or --offline.\\nIf it is not, use \\\"--fasta $ex_unpacked\\\"\\n\\n\" unless $QUIET;"," }",""," if($ftp) {"," $ftp-\u003ecwd('../');"," $ftp-\u003ecwd('../');"," }"," }","}","","# PLUGINS","#########","","sub plugins() {"," my $ok;",""," if($AUTO) {"," $ok = $AUTO =~ /p/i ? 'y' : 'n';"," }"," else {"," print \"\\nThe VEP can use plugins to add functionality and data.\\n\" unless $QUIET;"," print \"Plugins will be installed in $PLUGINS_DIR\\n\" unless $QUIET;",""," print \"Do you want to install any plugins (y/n)? \";",""," $ok = \u003c\u003e;"," }",""," if($ok !~ /^y/i) {"," print \"Skipping plugin installation\\n\" unless $QUIET;"," return;"," }",""," # check plugin installation dir exists"," if(!(-e $PLUGINS_DIR)) {"," if(!$AUTO) {"," print \"Plugins directory $PLUGINS_DIR does not exists - do you want to create it (y/n)? \";",""," my $ok = \u003c\u003e;",""," if($ok !~ /^y/i) {"," print \"Exiting\\n\";"," exit(0);"," }"," }",""," mkpath($PLUGINS_DIR) or die \"ERROR: Could not create directory $PLUGINS_DIR\\n\";"," }"," mkpath($PLUGINS_DIR) unless -e $PLUGINS_DIR;",""," my $plugin_url_root = $PLUGIN_URL.'/release/'.$API_VERSION;",""," # download and eval plugin config file"," my $plugin_config_file = $PLUGINS_DIR.'/plugin_config.txt';"," download_to_file($plugin_url_root.'/plugin_config.txt', $plugin_config_file);",""," die(\"ERROR: Could not access plugin config file $plugin_config_file\\n\") unless($plugin_config_file \u0026\u0026 -e $plugin_config_file);",""," open IN, $plugin_config_file;"," my @content = \u003cIN\u003e;"," close IN;",""," my $VEP_PLUGIN_CONFIG = eval join('', @content);"," die(\"ERROR: Could not eval VEP plugin config file: $@\\n\") if $@;"," my @plugins = @{$VEP_PLUGIN_CONFIG-\u003e{plugins}};",""," # get sections"," my @sections = grep {defined($_)} map {defined($_-\u003e{section}) ? $_-\u003e{section} : undef} @plugins;",""," # unique sort in same order"," my ($prev, @new);"," for(@sections) {"," if(!defined($prev) || $prev ne $_) {"," push @new, $_;"," }"," $prev = $_;"," }"," @sections = @new;"," push @sections, '';",""," # generate list to present to user"," my (%by_number, %by_key);"," my $i = 1;"," my $plugin_list = '';",""," # get length of longest label/key"," my $length = length((sort {length($a-\u003e{key}) \u003c=\u003e length($b-\u003e{key})} @plugins)[-1]-\u003e{key});",""," foreach my $section(@sections) {"," my $section_name = $section || (scalar @sections \u003e 1 ? 'Other plugins' : 'Plugins');",""," my @section_plugins;",""," # check that plugins have plugin_url defined"," # otherwise we can't download it"," if($section eq '') {"," @section_plugins = grep {$_-\u003e{plugin_url} \u0026\u0026 !defined($_-\u003e{section})} @plugins;"," }"," else {"," @section_plugins = grep {$_-\u003e{plugin_url} \u0026\u0026 defined($_-\u003e{section}) \u0026\u0026 $_-\u003e{section} eq $section} @plugins;"," }",""," next unless scalar @section_plugins;"," $plugin_list .= \"# $section_name\\n\";",""," $_-\u003e{plugin_number} = $i++ for @section_plugins;"," $by_number{$_-\u003e{plugin_number}} = $_ for @section_plugins;"," $by_key{lc($_-\u003e{key})} = $_ for @section_plugins;",""," $plugin_list .= sprintf("," \"%4i: %*s - %s\\n\","," $_-\u003e{plugin_number},"," 0 - $length,"," $_-\u003e{key},"," $_-\u003e{helptip} || ''"," ) for @section_plugins;"," }",""," # now establish which we are installing"," my (@indexes, @selected_plugins);",""," my $plugins_list = \"Available plugins: \" ."," join(\",\", sort map {$_-\u003e{key}} values %by_key) . \"\\n\";",""," # either from user input"," if(!$AUTO) {"," print \"\\nThe following plugins are available; which do you want (can specify multiple separated by spaces or 0 for all): \\n$plugin_list\\n? \";"," @indexes = split /\\s+/, \u003c\u003e;",""," # user wants all species found"," if(scalar @indexes == 1 \u0026\u0026 $indexes[0] == 0) {"," @indexes = 1..(scalar keys %by_number);"," }",""," @selected_plugins = map {$by_number{$_}} grep {$by_number{$_}} @indexes;"," }",""," # or from list passed on command line"," elsif (lc($PLUGINS-\u003e[0]) eq 'list') {"," # list the plugins and exit"," print \"\\n\" . $plugins_list;"," return;"," } elsif (lc($PLUGINS-\u003e[0]) eq 'all' || $PLUGINS-\u003e[0] eq '0') {"," # download all plugins"," @selected_plugins = sort {$a-\u003e{key} cmp $b-\u003e{key}} values %by_key;"," } else {"," # download specific plugins from command-line arguments"," my @not_found = grep {!$by_key{lc($_)}} @$PLUGINS;"," warn(\"\\nWARNING: The following plugins have not been found: \","," join(\",\", @not_found) . \"\\n\", $plugins_list, \"\\n\") if @not_found;"," @selected_plugins = map {$by_key{lc($_)}} grep {$by_key{lc($_)}} @$PLUGINS;"," }",""," if(!@selected_plugins) {"," printf(\"\\nERROR: No valid plugins given\\n\");"," return;"," }",""," # store a flag to warn user at end if any plugins require additional setup"," my $requires_install_or_data = 0;",""," foreach my $pl(@selected_plugins) {"," printf(\"\\n - installing \\\"%s\\\"\\n\", $pl-\u003e{key});",""," my $local_file = $PLUGINS_DIR.'/'.$pl-\u003e{key}.'.pm';",""," # overwrite?"," if(-e $local_file) {"," printf("," \"%s already installed; %s\","," $pl-\u003e{key},"," $AUTO ? \"overwriting\\n\" : \"do you want to overwrite (probably OK if updating) (y/n)? \""," );",""," my $ok = $AUTO ? 'y' : \u003c\u003e;",""," if($ok !~ /^y/i) {"," print \" - Skipping\\n\";"," next;"," }"," }",""," # download"," download_to_file($pl-\u003e{plugin_url}, $local_file);",""," # warn if failed"," unless(-e $local_file) {"," print \" - WARNING: Failed to download/install \".$pl-\u003e{key}.\"\\n\";"," next;"," }",""," # additional setup required?"," if($pl-\u003e{requires_install} || $pl-\u003e{requires_data}) {"," print \" - This plugin requires installation\\n\" if $pl-\u003e{requires_install};"," print \" - This plugin requires data\\n\" if $pl-\u003e{requires_data};"," print \" - See $local_file for details\\n\";",""," $requires_install_or_data = 1;"," }",""," else {"," printf("," \" - add \\\"--plugin %s%s\\\" to your VEP command to use this plugin\\n\","," $pl-\u003e{key},"," $pl-\u003e{params} ? ',[options]' : ''"," );"," }",""," print \" - OK\\n\";"," }",""," print \"\\nNB: One or more plugins that you have installed will not work without installation or downloading data; see logs above\\n\" if $requires_install_or_data;","}","","# OTHER SUBS","############","","sub download_to_file {"," my ($url, $file) = @_;",""," if($CAN_USE_CURL) {"," my $response = `curl -s -o $file -w '%{http_code}' --location \"$url\" `;"," if ( $response != 200 \u0026\u0026 $response != 226) {"," print \"curl failed ($response), trying to fetch using LWP::Simple\\n\" unless $QUIET;"," $CAN_USE_CURL = 0;"," download_to_file($url, $file);"," }"," }",""," elsif($CAN_USE_LWP) {"," my $response = getstore($url, $file);",""," unless($response == 200) {",""," # try no proxy"," $ua-\u003eno_proxy('github.com');",""," $response = getstore($url, $file);",""," unless($response == 200) {"," print \"LWP::Simple failed ($response), trying to fetch using HTTP::Tiny\\n\" unless $QUIET;"," $CAN_USE_LWP = 0;"," download_to_file($url, $file);"," }"," }"," }"," elsif($CAN_USE_HTTP_TINY) {"," my $response = HTTP::Tiny-\u003enew(no_proxy =\u003e 'github.com')-\u003eget($url);",""," if($response-\u003e{success}) {"," open OUT, \"\u003e$file\" or die \"Could not write to file $file\\n\";"," binmode OUT;"," print OUT $response-\u003e{content};"," close OUT;"," }"," else {"," #warn \"WARNING: Failed to fetch from $url\\nError code: $response-\u003e{reason}\\nError content:\\n$response-\u003e{content}\\nTrying without no_proxy\\n\" unless $QUIET;"," $response = HTTP::Tiny-\u003enew-\u003eget($url);",""," if($response-\u003e{success}) {"," open OUT, \"\u003e$file\" or die \"Could not write to file $file\\n\";"," binmode OUT;"," print OUT $response-\u003e{content};"," close OUT;"," }"," else {"," die(\"ERROR: Failed last resort of using HTTP::Tiny to download $url\\n\");"," }"," }"," }"," else {"," die(\"ERROR: Unable to download files without curl, LWP or HTTP::Tiny installed\\n\");"," }","}","","# unpack a tarball","sub unpack_arch {"," my ($arch_file, $dir) = @_;",""," if($CAN_USE_ARCHIVE) {"," my $ar = Archive::Extract-\u003enew(archive =\u003e $arch_file);"," my $ok = $ar-\u003eextract(to =\u003e $dir) or die $ar-\u003eerror;"," }"," else {"," if($arch_file =~ /.zip$/ \u0026\u0026 $CAN_USE_UNZIP) {"," system \"unzip -qq $arch_file -d $dir\" and die(\"ERROR: Failed to unpack file $arch_file\\n\");"," }"," elsif($arch_file =~ /(\\.tar\\.|\\.t)gz$/ \u0026\u0026 $CAN_USE_TAR) {"," system \"tar -C $dir -zxf $arch_file\" and die(\"ERROR: Failed to unpack file $arch_file\\n\");"," }"," elsif($arch_file =~ /\\.gz$/ \u0026\u0026 $arch_file !~ /(\\.tar\\.|\\.t)gz$/ \u0026\u0026 $CAN_USE_GZIP) {"," my $unpacked = $arch_file;"," $unpacked =~ s/.*\\///g;"," $unpacked =~ s/\\.gz$//;"," system \"gzip -dc $arch_file \u003e $dir/$unpacked\" and die(\"ERROR: Failed to unpack file $arch_file\\n\");"," }"," else {"," die(\"ERROR: Unable to unpack file $arch_file without Archive::Extract or tar/unzip/gzip\\n\");"," }"," }",""," unlink($arch_file);","}","","sub usage {"," my $versions = get_version_string();",""," my $usage =\u003c\u003cEND;","#---------------#","# VEP INSTALLER #","#---------------#","","versions"," $versions","","http://www.ensembl.org/info/docs/variation/vep/vep_script.html#installer","","Usage:","perl INSTALL.pl [arguments]","","Options","=======","","-h | --help Display this message and quit","","-d | --DESTDIR Set destination directory for API install (default = './')","--CACHE_VERSION Set data (cache, FASTA) version to install (default = $VERSION)","-c | --CACHEDIR Set destination directory for cache files (default = '$ENV{HOME}/.vep/')","","-a | --AUTO Run installer without user prompts. Use \"a\" (API + Faidx/htslib),"," \"l\" (Faidx/htslib only), \"c\" (cache), \"f\" (FASTA), \"p\" (plugins) to specify"," parts to install e.g. -a ac for API and cache","-n | --NO_UPDATE Do not check for updates to ensembl-vep or API","-s | --SPECIES Comma-separated list of species to install when using --AUTO","-y | --ASSEMBLY Assembly name to use if more than one during --AUTO","","--NO_PLUGINS Skip plugin installation","-g | --PLUGINS Comma-separated list of plugins to install when using --AUTO; you can also"," use \"list\" to list all plugins and \"all\" to install all available plugins","-r | --PLUGINSDIR Set destination directory for VEP plugins files (default = '$ENV{HOME}/.vep/Plugins/')","-q | --QUIET Do not write any status output when using --AUTO","-p | --PREFER_BIN Use this if the installer fails with out of memory errors","-l | --NO_HTSLIB Do not attempt to install Faidx/htslib","--NO_BIOPERL Do not install BioPerl","","-t | --CONVERT Convert downloaded caches to use tabix for retrieving"," co-located variants (requires tabix)","","","-u | --CACHEURL Override default cache URL; this may be a local directory or"," a remote (e.g. FTP) address.","-f | --FASTAURL Override default FASTA URL; this may be a local directory or"," a remote (e.g. FTP) address. The FASTA URL/directory must have"," gzipped FASTA files under the following structure:"," [species]/[dna]/","END",""," print 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data-line-number="946" class="react-line-number react-code-text" style="padding-right:16px">946</div><div data-line-number="947" class="react-line-number react-code-text" style="padding-right:16px">947</div><div data-line-number="948" class="react-line-number react-code-text" style="padding-right:16px">948</div><div data-line-number="949" class="react-line-number react-code-text" style="padding-right:16px">949</div><div data-line-number="950" class="react-line-number react-code-text" style="padding-right:16px">950</div><div data-line-number="951" class="react-line-number react-code-text" style="padding-right:16px">951</div><div data-line-number="952" class="react-line-number react-code-text" style="padding-right:16px">952</div><div data-line-number="953" class="react-line-number react-code-text" style="padding-right:16px">953</div><div data-line-number="954" class="react-line-number react-code-text" style="padding-right:16px">954</div><div data-line-number="955" class="react-line-number react-code-text" style="padding-right:16px">955</div><div data-line-number="956" class="react-line-number react-code-text" style="padding-right:16px">956</div><div data-line-number="957" class="react-line-number react-code-text" style="padding-right:16px">957</div><div data-line-number="958" class="react-line-number react-code-text" style="padding-right:16px">958</div><div data-line-number="959" class="react-line-number react-code-text" style="padding-right:16px">959</div><div data-line-number="960" class="react-line-number react-code-text" style="padding-right:16px">960</div><div data-line-number="961" class="react-line-number react-code-text" style="padding-right:16px">961</div><div data-line-number="962" class="react-line-number react-code-text" style="padding-right:16px">962</div><div data-line-number="963" class="react-line-number react-code-text" style="padding-right:16px">963</div><div data-line-number="964" class="react-line-number react-code-text" style="padding-right:16px">964</div><div data-line-number="965" class="react-line-number react-code-text" style="padding-right:16px">965</div><div data-line-number="966" class="react-line-number react-code-text" style="padding-right:16px">966</div><div data-line-number="967" class="react-line-number react-code-text" style="padding-right:16px">967</div><div data-line-number="968" class="react-line-number react-code-text" style="padding-right:16px">968</div><div data-line-number="969" class="react-line-number react-code-text" style="padding-right:16px">969</div><div data-line-number="970" class="react-line-number react-code-text" style="padding-right:16px">970</div><div data-line-number="971" class="react-line-number react-code-text" style="padding-right:16px">971</div><div data-line-number="972" class="react-line-number react-code-text" style="padding-right:16px">972</div><div data-line-number="973" class="react-line-number react-code-text" style="padding-right:16px">973</div><div data-line-number="974" class="react-line-number react-code-text" style="padding-right:16px">974</div><div data-line-number="975" class="react-line-number react-code-text" style="padding-right:16px">975</div><div data-line-number="976" class="react-line-number react-code-text" style="padding-right:16px">976</div><div data-line-number="977" class="react-line-number react-code-text" style="padding-right:16px">977</div><div data-line-number="978" class="react-line-number react-code-text" style="padding-right:16px">978</div><div data-line-number="979" class="react-line-number react-code-text" style="padding-right:16px">979</div><div data-line-number="980" class="react-line-number react-code-text" style="padding-right:16px">980</div><div data-line-number="981" class="react-line-number react-code-text" style="padding-right:16px">981</div><div data-line-number="982" class="react-line-number react-code-text" style="padding-right:16px">982</div><div data-line-number="983" class="react-line-number react-code-text" style="padding-right:16px">983</div><div data-line-number="984" class="react-line-number react-code-text" style="padding-right:16px">984</div><div data-line-number="985" class="react-line-number react-code-text" style="padding-right:16px">985</div><div data-line-number="986" class="react-line-number react-code-text" style="padding-right:16px">986</div><div data-line-number="987" class="react-line-number react-code-text" style="padding-right:16px">987</div><div data-line-number="988" class="react-line-number react-code-text" style="padding-right:16px">988</div><div data-line-number="989" class="react-line-number react-code-text" style="padding-right:16px">989</div><div data-line-number="990" class="react-line-number react-code-text" style="padding-right:16px">990</div><div data-line-number="991" class="react-line-number react-code-text" style="padding-right:16px">991</div><div data-line-number="992" class="react-line-number react-code-text" style="padding-right:16px">992</div><div data-line-number="993" class="react-line-number react-code-text" style="padding-right:16px">993</div><div data-line-number="994" class="react-line-number react-code-text" style="padding-right:16px">994</div><div data-line-number="995" class="react-line-number react-code-text" style="padding-right:16px">995</div><div data-line-number="996" class="react-line-number react-code-text" style="padding-right:16px">996</div><div data-line-number="997" class="react-line-number react-code-text" style="padding-right:16px">997</div><div data-line-number="998" class="react-line-number react-code-text" style="padding-right:16px">998</div><div data-line-number="999" class="react-line-number react-code-text" style="padding-right:16px">999</div><div data-line-number="1000" class="react-line-number react-code-text" style="padding-right:16px">1000</div></div><div class="react-code-lines"><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC1" class="react-file-line html-div" data-testid="code-cell" data-line-number="1" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>!/usr/bin/env perl</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC2" class="react-file-line html-div" data-testid="code-cell" data-line-number="2" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC3" class="react-file-line html-div" data-testid="code-cell" data-line-number="3" style="position:relative"><span class="pl-c"><span class="pl-k">=head1</span> <span class="pl-smi">LICENSE</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC4" class="react-file-line html-div" data-testid="code-cell" data-line-number="4" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC5" class="react-file-line html-div" data-testid="code-cell" data-line-number="5" style="position:relative"><span class="pl-c">Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC6" class="react-file-line html-div" data-testid="code-cell" data-line-number="6" style="position:relative"><span class="pl-c">Copyright [2016-2024] EMBL-European Bioinformatics Institute</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC7" class="react-file-line html-div" data-testid="code-cell" data-line-number="7" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC8" class="react-file-line html-div" data-testid="code-cell" data-line-number="8" style="position:relative"><span class="pl-c">Licensed under the Apache License, Version 2.0 (the "License");</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC9" class="react-file-line html-div" data-testid="code-cell" data-line-number="9" style="position:relative"><span class="pl-c">you may not use this file except in compliance with the License.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC10" class="react-file-line html-div" data-testid="code-cell" data-line-number="10" style="position:relative"><span class="pl-c">You may obtain a copy of the License at</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC11" class="react-file-line html-div" data-testid="code-cell" data-line-number="11" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC12" class="react-file-line html-div" data-testid="code-cell" data-line-number="12" style="position:relative"><span class="pl-c"> http://www.apache.org/licenses/LICENSE-2.0</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC13" class="react-file-line html-div" data-testid="code-cell" data-line-number="13" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC14" class="react-file-line html-div" data-testid="code-cell" data-line-number="14" style="position:relative"><span class="pl-c">Unless required by applicable law or agreed to in writing, software</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC15" class="react-file-line html-div" data-testid="code-cell" data-line-number="15" style="position:relative"><span class="pl-c">distributed under the License is distributed on an "AS IS" BASIS,</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC16" class="react-file-line html-div" data-testid="code-cell" data-line-number="16" style="position:relative"><span class="pl-c">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC17" class="react-file-line html-div" data-testid="code-cell" data-line-number="17" style="position:relative"><span class="pl-c">See the License for the specific language governing permissions and</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC18" class="react-file-line html-div" data-testid="code-cell" data-line-number="18" style="position:relative"><span class="pl-c">limitations under the License.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC19" class="react-file-line html-div" data-testid="code-cell" data-line-number="19" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC20" class="react-file-line html-div" data-testid="code-cell" data-line-number="20" style="position:relative"><span class="pl-c"><span class="pl-k">=cut</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC21" class="react-file-line html-div" data-testid="code-cell" data-line-number="21" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC22" class="react-file-line html-div" data-testid="code-cell" data-line-number="22" style="position:relative"><span class="pl-c"><span class="pl-k">=head1</span> <span class="pl-smi">CONTACT</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC23" class="react-file-line html-div" data-testid="code-cell" data-line-number="23" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC24" class="react-file-line html-div" data-testid="code-cell" data-line-number="24" style="position:relative"><span class="pl-c"> Please email comments or questions to the public Ensembl</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC25" class="react-file-line html-div" data-testid="code-cell" data-line-number="25" style="position:relative"><span class="pl-c"> developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC26" class="react-file-line html-div" data-testid="code-cell" data-line-number="26" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC27" class="react-file-line html-div" data-testid="code-cell" data-line-number="27" style="position:relative"><span class="pl-c"> Questions may also be sent to the Ensembl help desk at</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC28" class="react-file-line html-div" data-testid="code-cell" data-line-number="28" style="position:relative"><span class="pl-c"> <http://www.ensembl.org/Help/Contact>.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC29" class="react-file-line html-div" data-testid="code-cell" data-line-number="29" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC30" class="react-file-line html-div" data-testid="code-cell" data-line-number="30" style="position:relative"><span class="pl-c"><span class="pl-k">=cut</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC31" class="react-file-line html-div" data-testid="code-cell" data-line-number="31" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC32" class="react-file-line html-div" data-testid="code-cell" data-line-number="32" style="position:relative"><span class="pl-c"><span class="pl-k">=head1</span> <span class="pl-smi">NAME</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC33" class="react-file-line html-div" data-testid="code-cell" data-line-number="33" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC34" class="react-file-line html-div" data-testid="code-cell" data-line-number="34" style="position:relative"><span class="pl-c">INSTALL.pl - a script to install required code and data for VEP</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC35" class="react-file-line html-div" data-testid="code-cell" data-line-number="35" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC36" class="react-file-line html-div" data-testid="code-cell" data-line-number="36" style="position:relative"><span class="pl-c"><span class="pl-k">=cut</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC37" class="react-file-line html-div" data-testid="code-cell" data-line-number="37" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC38" class="react-file-line html-div" data-testid="code-cell" data-line-number="38" style="position:relative"><span class="pl-k">use</span> strict;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC39" class="react-file-line html-div" data-testid="code-cell" data-line-number="39" style="position:relative"><span class="pl-k">use</span> FindBin <span class="pl-s"><span class="pl-pds">qw(</span>$RealBin<span class="pl-pds">)</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC40" class="react-file-line html-div" data-testid="code-cell" data-line-number="40" style="position:relative"><span class="pl-k">use</span> lib <span class="pl-smi">$RealBin</span>.<span class="pl-s"><span class="pl-pds">'</span>/modules<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC41" class="react-file-line html-div" data-testid="code-cell" data-line-number="41" style="position:relative"><span class="pl-k">use</span> Getopt::Long;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC42" class="react-file-line html-div" data-testid="code-cell" data-line-number="42" style="position:relative"><span class="pl-k">use</span> File::Path <span class="pl-s"><span class="pl-pds">qw(</span>mkpath rmtree<span class="pl-pds">)</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC43" class="react-file-line html-div" data-testid="code-cell" data-line-number="43" style="position:relative"><span class="pl-k">use</span> File::Copy;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC44" class="react-file-line html-div" data-testid="code-cell" data-line-number="44" style="position:relative"><span class="pl-k">use</span> File::Basename;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC45" class="react-file-line html-div" data-testid="code-cell" data-line-number="45" style="position:relative"><span class="pl-k">use</span> Net::FTP;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC46" class="react-file-line html-div" data-testid="code-cell" data-line-number="46" style="position:relative"><span class="pl-k">use</span> Cwd;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC47" class="react-file-line html-div" data-testid="code-cell" data-line-number="47" style="position:relative"><span class="pl-k">use</span> Scalar::Util <span class="pl-s"><span class="pl-pds">qw(</span>looks_like_number<span class="pl-pds">)</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC48" class="react-file-line html-div" data-testid="code-cell" data-line-number="48" style="position:relative"><span class="pl-k">use</span> Bio::EnsEMBL::VEP::Utils <span class="pl-s"><span class="pl-pds">qw(</span>get_version_data get_version_string<span class="pl-pds">)</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC49" class="react-file-line html-div" data-testid="code-cell" data-line-number="49" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC50" class="react-file-line html-div" data-testid="code-cell" data-line-number="50" style="position:relative"><span class="pl-k">our</span> (</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC51" class="react-file-line html-div" data-testid="code-cell" data-line-number="51" style="position:relative"> <span class="pl-smi">$DEST_DIR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC52" class="react-file-line html-div" data-testid="code-cell" data-line-number="52" style="position:relative"> <span class="pl-smi">$ENS_CVS_ROOT</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC53" class="react-file-line html-div" data-testid="code-cell" data-line-number="53" style="position:relative"> <span class="pl-smi">$API_VERSION</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC54" class="react-file-line html-div" data-testid="code-cell" data-line-number="54" style="position:relative"> <span class="pl-smi">$DATA_VERSION</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC55" class="react-file-line html-div" data-testid="code-cell" data-line-number="55" style="position:relative"> <span class="pl-smi">$ASSEMBLY</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC56" class="react-file-line html-div" data-testid="code-cell" data-line-number="56" style="position:relative"> <span class="pl-smi">$ENS_GIT_ROOT</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC57" class="react-file-line html-div" data-testid="code-cell" data-line-number="57" style="position:relative"> <span class="pl-smi">$BIOPERL_URL</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC58" class="react-file-line html-div" data-testid="code-cell" data-line-number="58" style="position:relative"> <span class="pl-smi">$CACHE_URL</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC59" class="react-file-line html-div" data-testid="code-cell" data-line-number="59" style="position:relative"> <span class="pl-smi">$CACHE_URL_INDEXED</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC60" class="react-file-line html-div" data-testid="code-cell" data-line-number="60" style="position:relative"> <span class="pl-smi">$CACHE_DIR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC61" class="react-file-line html-div" data-testid="code-cell" data-line-number="61" style="position:relative"> <span class="pl-smi">$NO_PLUGINS</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC62" class="react-file-line html-div" data-testid="code-cell" data-line-number="62" style="position:relative"> <span class="pl-smi">$PLUGINS</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC63" class="react-file-line html-div" data-testid="code-cell" data-line-number="63" style="position:relative"> <span class="pl-smi">$PLUGIN_URL</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC64" class="react-file-line html-div" data-testid="code-cell" data-line-number="64" style="position:relative"> <span class="pl-smi">$PLUGINS_DIR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC65" class="react-file-line html-div" data-testid="code-cell" data-line-number="65" style="position:relative"> <span class="pl-smi">$FASTA_URL</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC66" class="react-file-line html-div" data-testid="code-cell" data-line-number="66" style="position:relative"> <span class="pl-smi">$FTP_USER</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC67" class="react-file-line html-div" data-testid="code-cell" data-line-number="67" style="position:relative"> <span class="pl-smi">$HELP</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC68" class="react-file-line html-div" data-testid="code-cell" data-line-number="68" style="position:relative"> <span class="pl-smi">$NO_UPDATE</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC69" class="react-file-line html-div" data-testid="code-cell" data-line-number="69" style="position:relative"> <span class="pl-smi">$SPECIES</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC70" class="react-file-line html-div" data-testid="code-cell" data-line-number="70" style="position:relative"> <span class="pl-smi">$AUTO</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC71" class="react-file-line html-div" data-testid="code-cell" data-line-number="71" style="position:relative"> <span class="pl-smi">$QUIET</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC72" class="react-file-line html-div" data-testid="code-cell" data-line-number="72" style="position:relative"> <span class="pl-smi">$PREFER_BIN</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC73" class="react-file-line html-div" data-testid="code-cell" data-line-number="73" style="position:relative"> <span class="pl-smi">$CONVERT</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC74" class="react-file-line html-div" data-testid="code-cell" data-line-number="74" style="position:relative"> <span class="pl-smi">$TEST</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC75" class="react-file-line html-div" data-testid="code-cell" data-line-number="75" style="position:relative"> <span class="pl-smi">$NO_HTSLIB</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC76" class="react-file-line html-div" data-testid="code-cell" data-line-number="76" style="position:relative"> <span class="pl-smi">$LIB_DIR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC77" class="react-file-line html-div" data-testid="code-cell" data-line-number="77" style="position:relative"> <span class="pl-smi">$HTSLIB_DIR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC78" class="react-file-line html-div" data-testid="code-cell" data-line-number="78" style="position:relative"> <span class="pl-smi">$BIODBHTS_DIR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC79" class="react-file-line html-div" data-testid="code-cell" data-line-number="79" style="position:relative"> <span class="pl-smi">$REALPATH_DEST_DIR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC80" class="react-file-line html-div" data-testid="code-cell" data-line-number="80" style="position:relative"> <span class="pl-smi">$NO_TEST</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC81" class="react-file-line html-div" data-testid="code-cell" data-line-number="81" style="position:relative"> <span class="pl-smi">$NO_BIOPERL</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC82" class="react-file-line html-div" data-testid="code-cell" data-line-number="82" style="position:relative"> <span class="pl-smi">$ua</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC83" class="react-file-line html-div" data-testid="code-cell" data-line-number="83" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC84" class="react-file-line html-div" data-testid="code-cell" data-line-number="84" style="position:relative"> <span class="pl-smi">$CAN_USE_CURL</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC85" class="react-file-line html-div" data-testid="code-cell" data-line-number="85" style="position:relative"> <span class="pl-smi">$CAN_USE_LWP</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC86" class="react-file-line html-div" data-testid="code-cell" data-line-number="86" style="position:relative"> <span class="pl-smi">$CAN_USE_HTTP_TINY</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC87" class="react-file-line html-div" data-testid="code-cell" data-line-number="87" style="position:relative"> <span class="pl-smi">$CAN_USE_ARCHIVE</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC88" class="react-file-line html-div" data-testid="code-cell" data-line-number="88" style="position:relative"> <span class="pl-smi">$CAN_USE_UNZIP</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC89" class="react-file-line html-div" data-testid="code-cell" data-line-number="89" style="position:relative"> <span class="pl-smi">$CAN_USE_GZIP</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC90" class="react-file-line html-div" data-testid="code-cell" data-line-number="90" style="position:relative"> <span class="pl-smi">$CAN_USE_TAR</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC91" class="react-file-line html-div" data-testid="code-cell" data-line-number="91" style="position:relative"> <span class="pl-smi">$CAN_USE_DBI</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC92" class="react-file-line html-div" data-testid="code-cell" data-line-number="92" style="position:relative"> <span class="pl-smi">$CAN_USE_DBD_MYSQL</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC93" class="react-file-line html-div" data-testid="code-cell" data-line-number="93" style="position:relative">);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC94" class="react-file-line html-div" data-testid="code-cell" data-line-number="94" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC95" class="react-file-line html-div" data-testid="code-cell" data-line-number="95" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC96" class="react-file-line html-div" data-testid="code-cell" data-line-number="96" style="position:relative"><span class="pl-c"><span class="pl-c">#</span># VERSIONS OF INSTALLED SOFTWARE</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC97" class="react-file-line html-div" data-testid="code-cell" data-line-number="97" style="position:relative"><span class="pl-c"><span class="pl-c">#</span># MAY BE UPDATED IF SUCCESSFULLY TESTED</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC98" class="react-file-line html-div" data-testid="code-cell" data-line-number="98" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#######################################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC99" class="react-file-line html-div" data-testid="code-cell" data-line-number="99" style="position:relative"><span class="pl-k">our</span> <span class="pl-smi">$HTSLIB_VERSION</span> = <span class="pl-s"><span class="pl-pds">'</span>1.9<span class="pl-pds">'</span></span>; <span class="pl-c"><span class="pl-c">#</span> latest release as of release/98</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC100" class="react-file-line html-div" data-testid="code-cell" data-line-number="100" style="position:relative"><span class="pl-k">our</span> <span class="pl-smi">$BIOHTS_VERSION</span> = <span class="pl-s"><span class="pl-pds">'</span>2.11<span class="pl-pds">'</span></span>; <span class="pl-c"><span class="pl-c">#</span> latest 2.X release as of release/98</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC101" class="react-file-line html-div" data-testid="code-cell" data-line-number="101" style="position:relative"><span class="pl-k">our</span> <span class="pl-smi">$BIOPERL_VERSION</span> = <span class="pl-s"><span class="pl-pds">'</span>release-1-6-924<span class="pl-pds">'</span></span>; <span class="pl-c"><span class="pl-c">#</span> frozen, no pressing need to update</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC102" class="react-file-line html-div" data-testid="code-cell" data-line-number="102" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC103" class="react-file-line html-div" data-testid="code-cell" data-line-number="103" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC104" class="react-file-line html-div" data-testid="code-cell" data-line-number="104" style="position:relative"><span class="pl-c"><span class="pl-c">#</span># BEGIN BLOCK, CHECK WHAT MODULES ETC WE CAN USE</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC105" class="react-file-line html-div" data-testid="code-cell" data-line-number="105" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>################################################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC106" class="react-file-line html-div" data-testid="code-cell" data-line-number="106" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC107" class="react-file-line html-div" data-testid="code-cell" data-line-number="107" style="position:relative"><span class="pl-en">BEGIN</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC108" class="react-file-line html-div" data-testid="code-cell" data-line-number="108" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-k">eval</span> <span class="pl-s"><span class="pl-pds">q{</span> use LWP::Simple qw(getstore get $ua); 1 <span class="pl-pds">}</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC109" class="react-file-line html-div" data-testid="code-cell" data-line-number="109" style="position:relative"> <span class="pl-smi">$CAN_USE_LWP</span> = 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC110" class="react-file-line html-div" data-testid="code-cell" data-line-number="110" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC111" class="react-file-line html-div" data-testid="code-cell" data-line-number="111" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> set up a user agent's proxy (excluding github)</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC112" class="react-file-line html-div" data-testid="code-cell" data-line-number="112" style="position:relative"> <span class="pl-smi">$ua</span><span class="pl-k">-></span>env_proxy;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC113" class="react-file-line html-div" data-testid="code-cell" data-line-number="113" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC114" class="react-file-line html-div" data-testid="code-cell" data-line-number="114" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC115" class="react-file-line html-div" data-testid="code-cell" data-line-number="115" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-k">eval</span> <span class="pl-s"><span class="pl-pds">q{</span> use DBI; 1 <span class="pl-pds">}</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC116" class="react-file-line html-div" data-testid="code-cell" data-line-number="116" style="position:relative"> <span class="pl-smi">$CAN_USE_DBI</span> = 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC117" class="react-file-line html-div" data-testid="code-cell" data-line-number="117" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC118" class="react-file-line html-div" data-testid="code-cell" data-line-number="118" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC119" class="react-file-line html-div" data-testid="code-cell" data-line-number="119" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-k">eval</span> <span class="pl-s"><span class="pl-pds">q{</span> use DBD::mysql; 1 <span class="pl-pds">}</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC120" class="react-file-line html-div" data-testid="code-cell" data-line-number="120" style="position:relative"> <span class="pl-smi">$CAN_USE_DBD_MYSQL</span> = 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC121" class="react-file-line html-div" data-testid="code-cell" data-line-number="121" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC122" class="react-file-line html-div" data-testid="code-cell" data-line-number="122" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC123" class="react-file-line html-div" data-testid="code-cell" data-line-number="123" style="position:relative"> <span class="pl-smi">$CAN_USE_CURL</span> = 1 <span class="pl-k">if</span> <span class="pl-s"><span class="pl-pds">`</span>which curl<span class="pl-pds">`</span></span> =~ <span class="pl-sr"><span class="pl-pds">/</span><span class="pl-cce">\/</span>curl<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC124" class="react-file-line html-div" data-testid="code-cell" data-line-number="124" style="position:relative"> <span class="pl-smi">$CAN_USE_HTTP_TINY</span> = 1 <span class="pl-k">if</span> <span class="pl-k">eval</span> <span class="pl-s"><span class="pl-pds">q{</span> use HTTP::Tiny; 1 <span class="pl-pds">}</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC125" class="react-file-line html-div" data-testid="code-cell" data-line-number="125" style="position:relative"> <span class="pl-smi">$CAN_USE_ARCHIVE</span> = 1 <span class="pl-k">if</span> <span class="pl-k">eval</span> <span class="pl-s"><span class="pl-pds">q{</span> use Archive::Extract; 1 <span class="pl-pds">}</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC126" class="react-file-line html-div" data-testid="code-cell" data-line-number="126" style="position:relative"> <span class="pl-smi">$CAN_USE_UNZIP</span> = 1 <span class="pl-k">if</span> <span class="pl-s"><span class="pl-pds">`</span>which unzip<span class="pl-pds">`</span></span> =~ <span class="pl-sr"><span class="pl-pds">/</span><span class="pl-cce">\/</span>unzip<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC127" class="react-file-line html-div" data-testid="code-cell" data-line-number="127" style="position:relative"> <span class="pl-smi">$CAN_USE_GZIP</span> = 1 <span class="pl-k">if</span> <span class="pl-s"><span class="pl-pds">`</span>which gzip<span class="pl-pds">`</span></span> =~ <span class="pl-sr"><span class="pl-pds">/</span><span class="pl-cce">\/</span>gzip<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC128" class="react-file-line html-div" data-testid="code-cell" data-line-number="128" style="position:relative"> <span class="pl-smi">$CAN_USE_TAR</span> = 1 <span class="pl-k">if</span> <span class="pl-s"><span class="pl-pds">`</span>which tar<span class="pl-pds">`</span></span> =~ <span class="pl-sr"><span class="pl-pds">/</span><span class="pl-cce">\/</span>tar<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC129" class="react-file-line html-div" data-testid="code-cell" data-line-number="129" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC130" class="react-file-line html-div" data-testid="code-cell" data-line-number="130" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC131" class="react-file-line html-div" data-testid="code-cell" data-line-number="131" style="position:relative"><span class="pl-smi">$|</span> = 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC132" class="react-file-line html-div" data-testid="code-cell" data-line-number="132" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC133" class="react-file-line html-div" data-testid="code-cell" data-line-number="133" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> CONFIGURE</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC134" class="react-file-line html-div" data-testid="code-cell" data-line-number="134" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>##########</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC135" class="react-file-line html-div" data-testid="code-cell" data-line-number="135" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC136" class="react-file-line html-div" data-testid="code-cell" data-line-number="136" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> other global data</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC137" class="react-file-line html-div" data-testid="code-cell" data-line-number="137" style="position:relative"><span class="pl-k">my</span> <span class="pl-smi">@API_MODULES</span> = (</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC138" class="react-file-line html-div" data-testid="code-cell" data-line-number="138" style="position:relative"> { <span class="pl-c1">name</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>ensembl<span class="pl-pds">'</span></span>, <span class="pl-c1">path</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span> <span class="pl-pds">'</span></span>, <span class="pl-c1">test_pm</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Bio::EnsEMBL::Registry<span class="pl-pds">'</span></span> },</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC139" class="react-file-line html-div" data-testid="code-cell" data-line-number="139" style="position:relative"> { <span class="pl-c1">name</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>ensembl-variation<span class="pl-pds">'</span></span>, <span class="pl-c1">path</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Variation<span class="pl-pds">'</span></span>, <span class="pl-c1">test_pm</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Bio::EnsEMBL::Variation::Variation<span class="pl-pds">'</span></span> },</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC140" class="react-file-line html-div" data-testid="code-cell" data-line-number="140" style="position:relative"> { <span class="pl-c1">name</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>ensembl-funcgen<span class="pl-pds">'</span></span>, <span class="pl-c1">path</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Funcgen<span class="pl-pds">'</span></span>, <span class="pl-c1">test_pm</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Bio::EnsEMBL::Funcgen::RegulatoryFeature<span class="pl-pds">'</span></span> },</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC141" class="react-file-line html-div" data-testid="code-cell" data-line-number="141" style="position:relative"> { <span class="pl-c1">name</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>ensembl-compara<span class="pl-pds">'</span></span>, <span class="pl-c1">path</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Compara<span class="pl-pds">'</span></span>, <span class="pl-c1">test_pm</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Bio::EnsEMBL::Compara::Homology<span class="pl-pds">'</span></span> },</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC142" class="react-file-line html-div" data-testid="code-cell" data-line-number="142" style="position:relative"> { <span class="pl-c1">name</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>ensembl-io<span class="pl-pds">'</span></span>, <span class="pl-c1">path</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>IO,Utils<span class="pl-pds">'</span></span>, <span class="pl-c1">test_pm</span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>Bio::EnsEMBL::IO::Parser<span class="pl-pds">'</span></span> },</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC143" class="react-file-line html-div" data-testid="code-cell" data-line-number="143" style="position:relative">);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC144" class="react-file-line html-div" data-testid="code-cell" data-line-number="144" style="position:relative"><span class="pl-k">my</span> <span class="pl-smi">$ensembl_url_tail</span> = <span class="pl-s"><span class="pl-pds">'</span>/archive/<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC145" class="react-file-line html-div" data-testid="code-cell" data-line-number="145" style="position:relative"><span class="pl-k">my</span> <span class="pl-smi">$archive_type</span> = <span class="pl-s"><span class="pl-pds">'</span>.zip<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC146" class="react-file-line html-div" data-testid="code-cell" data-line-number="146" style="position:relative"><span class="pl-k">my</span> <span class="pl-smi">$git_api_root</span> = <span class="pl-s"><span class="pl-pds">'</span>https://api.github.com/repos/Ensembl/<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC147" class="react-file-line html-div" data-testid="code-cell" data-line-number="147" style="position:relative"><span class="pl-k">my</span> <span class="pl-smi">$VEP_MODULE_NAME</span> = <span class="pl-s"><span class="pl-pds">'</span>ensembl-vep<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC148" class="react-file-line html-div" data-testid="code-cell" data-line-number="148" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC149" class="react-file-line html-div" data-testid="code-cell" data-line-number="149" style="position:relative"><span class="pl-k">our</span> (<span class="pl-smi">@store_species</span>, <span class="pl-smi">@indexes</span>, <span class="pl-smi">@files</span>, <span class="pl-smi">$ftp</span>, <span class="pl-smi">$dirname</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC150" class="react-file-line html-div" data-testid="code-cell" data-line-number="150" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC151" class="react-file-line html-div" data-testid="code-cell" data-line-number="151" style="position:relative"><span class="pl-k">my</span> <span class="pl-smi">$config</span> = {};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC152" class="react-file-line html-div" data-testid="code-cell" data-line-number="152" style="position:relative">GetOptions(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC153" class="react-file-line html-div" data-testid="code-cell" data-line-number="153" style="position:relative"> <span class="pl-smi">$config</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC154" class="react-file-line html-div" data-testid="code-cell" data-line-number="154" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>DESTDIR|DEST_DIR|d=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC155" class="react-file-line html-div" data-testid="code-cell" data-line-number="155" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>CACHE_VERSION|e=i<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC156" class="react-file-line html-div" data-testid="code-cell" data-line-number="156" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>ASSEMBLY|y=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC157" class="react-file-line html-div" data-testid="code-cell" data-line-number="157" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>BIOPERL|BIOPERL_URL|b=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC158" class="react-file-line html-div" data-testid="code-cell" data-line-number="158" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>CACHEURL|CACHE_URL|u=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC159" class="react-file-line html-div" data-testid="code-cell" data-line-number="159" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>CACHEDIR|CACHE_DIR|c=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC160" class="react-file-line html-div" data-testid="code-cell" data-line-number="160" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>FASTAURL|FASTA_URL|f=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC161" class="react-file-line html-div" data-testid="code-cell" data-line-number="161" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>HELP|h<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC162" class="react-file-line html-div" data-testid="code-cell" data-line-number="162" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>NO_UPDATE|n<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC163" class="react-file-line html-div" data-testid="code-cell" data-line-number="163" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>SPECIES|s=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC164" class="react-file-line html-div" data-testid="code-cell" data-line-number="164" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>NO_PLUGINS<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC165" class="react-file-line html-div" data-testid="code-cell" data-line-number="165" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>PLUGINS|g=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC166" class="react-file-line html-div" data-testid="code-cell" data-line-number="166" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>PLUGINSDIR|PLUGINS_DIR|r=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC167" class="react-file-line html-div" data-testid="code-cell" data-line-number="167" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>PLUGINURL|PLUGIN_URL=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC168" class="react-file-line html-div" data-testid="code-cell" data-line-number="168" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>AUTO|a=s<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC169" class="react-file-line html-div" data-testid="code-cell" data-line-number="169" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>QUIET|q<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC170" class="react-file-line html-div" data-testid="code-cell" data-line-number="170" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>PREFER_BIN|p<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC171" class="react-file-line html-div" data-testid="code-cell" data-line-number="171" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>CONVERT|t<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC172" class="react-file-line html-div" data-testid="code-cell" data-line-number="172" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>TEST<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC173" class="react-file-line html-div" data-testid="code-cell" data-line-number="173" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>NO_HTSLIB|l<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC174" class="react-file-line html-div" data-testid="code-cell" data-line-number="174" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>NO_TEST<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC175" class="react-file-line html-div" data-testid="code-cell" data-line-number="175" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>NO_BIOPERL<span class="pl-pds">'</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC176" class="react-file-line html-div" data-testid="code-cell" data-line-number="176" style="position:relative">) <span class="pl-k">or</span> <span class="pl-k">die</span>(<span class="pl-s"><span class="pl-pds">"</span>ERROR: Failed to parse arguments<span class="pl-pds">"</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC177" class="react-file-line html-div" data-testid="code-cell" data-line-number="177" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC178" class="react-file-line html-div" data-testid="code-cell" data-line-number="178" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> Read configuration from environment variables starting with VEP_</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC179" class="react-file-line html-div" data-testid="code-cell" data-line-number="179" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> Priority is given to command-line arguments</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC180" class="react-file-line html-div" data-testid="code-cell" data-line-number="180" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">read_config_from_environment</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC181" class="react-file-line html-div" data-testid="code-cell" data-line-number="181" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$config</span> = <span class="pl-c1">shift</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC182" class="react-file-line html-div" data-testid="code-cell" data-line-number="182" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC183" class="react-file-line html-div" data-testid="code-cell" data-line-number="183" style="position:relative"> <span class="pl-k">for</span> <span class="pl-k">my</span> <span class="pl-smi">$key</span> (<span class="pl-c1">keys</span> <span class="pl-smi">%ENV</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC184" class="react-file-line html-div" data-testid="code-cell" data-line-number="184" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> Look for environment variables that start with VEP_</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC185" class="react-file-line html-div" data-testid="code-cell" data-line-number="185" style="position:relative"> <span class="pl-k">next</span> <span class="pl-k">unless</span> <span class="pl-smi">$key</span> =~ <span class="pl-s"><span class="pl-pds">"</span>^VEP_<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC186" class="react-file-line html-div" data-testid="code-cell" data-line-number="186" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC187" class="react-file-line html-div" data-testid="code-cell" data-line-number="187" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> Avoid setting empty strings</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC188" class="react-file-line html-div" data-testid="code-cell" data-line-number="188" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$value</span> = <span class="pl-smi">$ENV</span>{<span class="pl-smi">$key</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC189" class="react-file-line html-div" data-testid="code-cell" data-line-number="189" style="position:relative"> <span class="pl-k">next</span> <span class="pl-k">if</span> <span class="pl-smi">$value</span> <span class="pl-c1">eq</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC190" class="react-file-line html-div" data-testid="code-cell" data-line-number="190" style="position:relative"> <span class="pl-smi">$key</span> =~ <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">s</span>/</span>^VEP_</span><span class="pl-sr"><span class="pl-pds">//</span></span><span class="pl-sr"><span class="pl-pds"><span class="pl-k">ig</span></span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC191" class="react-file-line html-div" data-testid="code-cell" data-line-number="191" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC192" class="react-file-line html-div" data-testid="code-cell" data-line-number="192" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> Prioritise previous values</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC193" class="react-file-line html-div" data-testid="code-cell" data-line-number="193" style="position:relative"> <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-smi">$key</span>} ||= <span class="pl-smi">$value</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC194" class="react-file-line html-div" data-testid="code-cell" data-line-number="194" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC195" class="react-file-line html-div" data-testid="code-cell" data-line-number="195" style="position:relative"> <span class="pl-k">return</span> <span class="pl-smi">$config</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC196" class="react-file-line html-div" data-testid="code-cell" data-line-number="196" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC197" class="react-file-line html-div" data-testid="code-cell" data-line-number="197" style="position:relative"><span class="pl-smi">$config</span> = read_config_from_environment(<span class="pl-smi">$config</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC198" class="react-file-line html-div" data-testid="code-cell" data-line-number="198" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC199" class="react-file-line html-div" data-testid="code-cell" data-line-number="199" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> Quick fix: this script should use $config instead of multiple global variables</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC200" class="react-file-line html-div" data-testid="code-cell" data-line-number="200" style="position:relative"><span class="pl-smi">$DEST_DIR</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">DESTDIR</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC201" class="react-file-line html-div" data-testid="code-cell" data-line-number="201" style="position:relative"><span class="pl-smi">$DATA_VERSION</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">CACHE_VERSION</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC202" class="react-file-line html-div" data-testid="code-cell" data-line-number="202" style="position:relative"><span class="pl-smi">$ASSEMBLY</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">ASSEMBLY</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC203" class="react-file-line html-div" data-testid="code-cell" data-line-number="203" style="position:relative"><span class="pl-smi">$BIOPERL_URL</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">BIOPERL</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC204" class="react-file-line html-div" data-testid="code-cell" data-line-number="204" style="position:relative"><span class="pl-smi">$CACHE_URL</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">CACHEURL</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC205" class="react-file-line html-div" data-testid="code-cell" data-line-number="205" style="position:relative"><span class="pl-smi">$CACHE_DIR</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">CACHEDIR</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC206" class="react-file-line html-div" data-testid="code-cell" data-line-number="206" style="position:relative"><span class="pl-smi">$FASTA_URL</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">FASTAURL</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC207" class="react-file-line html-div" data-testid="code-cell" data-line-number="207" style="position:relative"><span class="pl-smi">$HELP</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">HELP</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC208" class="react-file-line html-div" data-testid="code-cell" data-line-number="208" style="position:relative"><span class="pl-smi">$NO_UPDATE</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">NO_UPDATE</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC209" class="react-file-line html-div" data-testid="code-cell" data-line-number="209" style="position:relative"><span class="pl-smi">$SPECIES</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">SPECIES</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC210" class="react-file-line html-div" data-testid="code-cell" data-line-number="210" style="position:relative"><span class="pl-smi">$NO_PLUGINS</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">NO_PLUGINS</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC211" class="react-file-line html-div" data-testid="code-cell" data-line-number="211" style="position:relative"><span class="pl-smi">$PLUGINS</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">PLUGINS</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC212" class="react-file-line html-div" data-testid="code-cell" data-line-number="212" style="position:relative"><span class="pl-smi">$PLUGINS_DIR</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">PLUGINSDIR</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC213" class="react-file-line html-div" data-testid="code-cell" data-line-number="213" style="position:relative"><span class="pl-smi">$PLUGIN_URL</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">PLUGINURL</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC214" class="react-file-line html-div" data-testid="code-cell" data-line-number="214" style="position:relative"><span class="pl-smi">$AUTO</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">AUTO</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC215" class="react-file-line html-div" data-testid="code-cell" data-line-number="215" style="position:relative"><span class="pl-smi">$QUIET</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">QUIET</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC216" class="react-file-line html-div" data-testid="code-cell" data-line-number="216" style="position:relative"><span class="pl-smi">$PREFER_BIN</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">PREFER_BIN</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC217" class="react-file-line html-div" data-testid="code-cell" data-line-number="217" style="position:relative"><span class="pl-smi">$CONVERT</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">CONVERT</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC218" class="react-file-line html-div" data-testid="code-cell" data-line-number="218" style="position:relative"><span class="pl-smi">$TEST</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">TEST</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC219" class="react-file-line html-div" data-testid="code-cell" data-line-number="219" style="position:relative"><span class="pl-smi">$NO_HTSLIB</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">NO_HTSLIB</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC220" class="react-file-line html-div" data-testid="code-cell" data-line-number="220" style="position:relative"><span class="pl-smi">$NO_TEST</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">NO_TEST</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC221" class="react-file-line html-div" data-testid="code-cell" data-line-number="221" style="position:relative"><span class="pl-smi">$NO_BIOPERL</span> ||= <span class="pl-smi">$config</span><span class="pl-k">-></span>{<span class="pl-c1">NO_BIOPERL</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC222" class="react-file-line html-div" data-testid="code-cell" data-line-number="222" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC223" class="react-file-line html-div" data-testid="code-cell" data-line-number="223" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> load version data</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC224" class="react-file-line html-div" data-testid="code-cell" data-line-number="224" style="position:relative"><span class="pl-k">our</span> <span class="pl-smi">$CURRENT_VERSION_DATA</span> = get_version_data(<span class="pl-smi">$RealBin</span>.<span class="pl-s"><span class="pl-pds">'</span>/.version<span class="pl-pds">'</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC225" class="react-file-line html-div" data-testid="code-cell" data-line-number="225" style="position:relative"><span class="pl-k">our</span> <span class="pl-smi">$VERSION</span> = <span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-smi">$VEP_MODULE_NAME</span>}<span class="pl-k">-></span>{<span class="pl-c1">release</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC226" class="react-file-line html-div" data-testid="code-cell" data-line-number="226" style="position:relative"><span class="pl-smi">$VERSION</span> =~ <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">s</span>/</span>release<span class="pl-cce">\/</span></span><span class="pl-sr"><span class="pl-pds">//</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC227" class="react-file-line html-div" data-testid="code-cell" data-line-number="227" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC228" class="react-file-line html-div" data-testid="code-cell" data-line-number="228" style="position:relative"><span class="pl-k">if</span>(<span class="pl-smi">$HELP</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC229" class="react-file-line html-div" data-testid="code-cell" data-line-number="229" style="position:relative"> usage();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC230" class="react-file-line html-div" data-testid="code-cell" data-line-number="230" style="position:relative"> <span class="pl-k">exit</span>(0);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC231" class="react-file-line html-div" data-testid="code-cell" data-line-number="231" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC232" class="react-file-line html-div" data-testid="code-cell" data-line-number="232" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC233" class="react-file-line html-div" data-testid="code-cell" data-line-number="233" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> check user has DBI and DBD::mysql</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC234" class="react-file-line html-div" data-testid="code-cell" data-line-number="234" style="position:relative"><span class="pl-k">die</span>(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC235" class="react-file-line html-div" data-testid="code-cell" data-line-number="235" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>ERROR: DBI module not found. VEP requires the DBI perl module to function<span class="pl-cce">\n\n</span><span class="pl-pds">"</span></span>.</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC236" class="react-file-line html-div" data-testid="code-cell" data-line-number="236" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements<span class="pl-cce">\n</span><span class="pl-pds">"</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC237" class="react-file-line html-div" data-testid="code-cell" data-line-number="237" style="position:relative">) <span class="pl-k">unless</span> <span class="pl-smi">$CAN_USE_DBI</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC238" class="react-file-line html-div" data-testid="code-cell" data-line-number="238" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC239" class="react-file-line html-div" data-testid="code-cell" data-line-number="239" style="position:relative"><span class="pl-c1">warn</span>(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC240" class="react-file-line html-div" data-testid="code-cell" data-line-number="240" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>WARNING: DBD::mysql module not found. VEP can only run in offline (--offline) mode without DBD::mysql installed<span class="pl-cce">\n\n</span><span class="pl-pds">"</span></span>.</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC241" class="react-file-line html-div" data-testid="code-cell" data-line-number="241" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#requirements<span class="pl-cce">\n</span><span class="pl-pds">"</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC242" class="react-file-line html-div" data-testid="code-cell" data-line-number="242" style="position:relative">) <span class="pl-k">unless</span> <span class="pl-smi">$CAN_USE_DBD_MYSQL</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC243" class="react-file-line html-div" data-testid="code-cell" data-line-number="243" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC244" class="react-file-line html-div" data-testid="code-cell" data-line-number="244" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC245" class="react-file-line html-div" data-testid="code-cell" data-line-number="245" style="position:relative"><span class="pl-k">my</span> <span class="pl-smi">$default_dir_used</span> = check_default_dir();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC246" class="react-file-line html-div" data-testid="code-cell" data-line-number="246" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC247" class="react-file-line html-div" data-testid="code-cell" data-line-number="247" style="position:relative"><span class="pl-smi">$LIB_DIR</span> = <span class="pl-smi">$DEST_DIR</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC248" class="react-file-line html-div" data-testid="code-cell" data-line-number="248" style="position:relative"><span class="pl-smi">$HTSLIB_DIR</span> = <span class="pl-smi">$LIB_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/htslib<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC249" class="react-file-line html-div" data-testid="code-cell" data-line-number="249" style="position:relative"><span class="pl-smi">$BIODBHTS_DIR</span> = <span class="pl-smi">$LIB_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/biodbhts<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC250" class="react-file-line html-div" data-testid="code-cell" data-line-number="250" style="position:relative"><span class="pl-smi">$REALPATH_DEST_DIR</span> .= Cwd::realpath(<span class="pl-smi">$DEST_DIR</span>).<span class="pl-s"><span class="pl-pds">'</span>/Bio<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC251" class="react-file-line html-div" data-testid="code-cell" data-line-number="251" style="position:relative"><span class="pl-smi">$DEST_DIR</span> .= <span class="pl-s"><span class="pl-pds">'</span>/Bio<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC252" class="react-file-line html-div" data-testid="code-cell" data-line-number="252" style="position:relative"><span class="pl-smi">$dirname</span> = dirname(<span class="pl-c1">__FILE__</span>) || <span class="pl-s"><span class="pl-pds">'</span>.<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC253" class="react-file-line html-div" data-testid="code-cell" data-line-number="253" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC254" class="react-file-line html-div" data-testid="code-cell" data-line-number="254" style="position:relative"><span class="pl-smi">$ENS_GIT_ROOT</span> ||= <span class="pl-s"><span class="pl-pds">'</span>https://github.com/Ensembl/<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC255" class="react-file-line html-div" data-testid="code-cell" data-line-number="255" style="position:relative"><span class="pl-smi">$BIOPERL_URL</span> ||= <span class="pl-s"><span class="pl-pds">"</span>https://github.com/bioperl/bioperl-live/archive/<span class="pl-smi">$BIOPERL_VERSION</span>.zip<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC256" class="react-file-line html-div" data-testid="code-cell" data-line-number="256" style="position:relative"><span class="pl-smi">$API_VERSION</span> ||= <span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-smi">$VEP_MODULE_NAME</span>}<span class="pl-k">-></span>{<span class="pl-c1">release</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC257" class="react-file-line html-div" data-testid="code-cell" data-line-number="257" style="position:relative"><span class="pl-smi">$DATA_VERSION</span> ||= <span class="pl-smi">$API_VERSION</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC258" class="react-file-line html-div" data-testid="code-cell" data-line-number="258" style="position:relative"><span class="pl-smi">$CACHE_DIR</span> ||= <span class="pl-smi">$ENV</span>{<span class="pl-c1">HOME</span>} ? <span class="pl-smi">$ENV</span>{<span class="pl-c1">HOME</span>}.<span class="pl-s"><span class="pl-pds">'</span>/.vep<span class="pl-pds">'</span></span> : <span class="pl-s"><span class="pl-pds">'</span>cache<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC259" class="react-file-line html-div" data-testid="code-cell" data-line-number="259" style="position:relative"><span class="pl-smi">$PLUGINS_DIR</span> ||= <span class="pl-smi">$CACHE_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/Plugins<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC260" class="react-file-line html-div" data-testid="code-cell" data-line-number="260" style="position:relative"><span class="pl-smi">$FTP_USER</span> ||= <span class="pl-s"><span class="pl-pds">'</span>anonymous<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC261" class="react-file-line html-div" data-testid="code-cell" data-line-number="261" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC262" class="react-file-line html-div" data-testid="code-cell" data-line-number="262" style="position:relative"><span class="pl-c"><span class="pl-c">#</span># Set the indexed cache url if it's been overwritten by the user</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC263" class="react-file-line html-div" data-testid="code-cell" data-line-number="263" style="position:relative"><span class="pl-smi">$CACHE_URL_INDEXED</span> = <span class="pl-smi">$CACHE_URL</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC264" class="react-file-line html-div" data-testid="code-cell" data-line-number="264" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC265" class="react-file-line html-div" data-testid="code-cell" data-line-number="265" style="position:relative"><span class="pl-smi">$CACHE_URL</span> ||= <span class="pl-s"><span class="pl-pds">"</span>https://ftp.ensembl.org/pub/release-<span class="pl-smi">$DATA_VERSION</span>/variation/vep<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC266" class="react-file-line html-div" data-testid="code-cell" data-line-number="266" style="position:relative"><span class="pl-smi">$CACHE_URL_INDEXED</span> ||= <span class="pl-s"><span class="pl-pds">"</span>https://ftp.ensembl.org/pub/release-<span class="pl-smi">$DATA_VERSION</span>/variation/indexed_vep_cache<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC267" class="react-file-line html-div" data-testid="code-cell" data-line-number="267" style="position:relative"><span class="pl-smi">$FASTA_URL</span> ||= <span class="pl-s"><span class="pl-pds">"</span>https://ftp.ensembl.org/pub/release-<span class="pl-smi">$DATA_VERSION</span>/fasta/<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC268" class="react-file-line html-div" data-testid="code-cell" data-line-number="268" style="position:relative"><span class="pl-smi">$PLUGIN_URL</span> ||= <span class="pl-s"><span class="pl-pds">'</span>https://raw.githubusercontent.com/Ensembl/VEP_plugins<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC269" class="react-file-line html-div" data-testid="code-cell" data-line-number="269" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC270" class="react-file-line html-div" data-testid="code-cell" data-line-number="270" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> using PREFER_BIN can save memory when extracting archives</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC271" class="react-file-line html-div" data-testid="code-cell" data-line-number="271" style="position:relative"><span class="pl-smi">$PREFER_BIN</span> = 0 <span class="pl-k">unless</span> <span class="pl-c1">defined</span>(<span class="pl-smi">$PREFER_BIN</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC272" class="react-file-line html-div" data-testid="code-cell" data-line-number="272" style="position:relative"><span class="pl-smi">$Archive::Extract::PREFER_BIN</span> = <span class="pl-smi">$PREFER_BIN</span> == 0 ? 0 : 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC273" class="react-file-line html-div" data-testid="code-cell" data-line-number="273" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC274" class="react-file-line html-div" data-testid="code-cell" data-line-number="274" style="position:relative"><span class="pl-smi">$QUIET</span> = 0 <span class="pl-k">unless</span> <span class="pl-smi">$AUTO</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC275" class="react-file-line html-div" data-testid="code-cell" data-line-number="275" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC276" class="react-file-line html-div" data-testid="code-cell" data-line-number="276" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> updates to ensembl-vep available?</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC277" class="react-file-line html-div" data-testid="code-cell" data-line-number="277" style="position:relative">update() <span class="pl-k">unless</span> <span class="pl-smi">$NO_UPDATE</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC278" class="react-file-line html-div" data-testid="code-cell" data-line-number="278" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC279" class="react-file-line html-div" data-testid="code-cell" data-line-number="279" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> auto?</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC280" class="react-file-line html-div" data-testid="code-cell" data-line-number="280" style="position:relative"><span class="pl-k">if</span>(<span class="pl-smi">$AUTO</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC281" class="react-file-line html-div" data-testid="code-cell" data-line-number="281" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC282" class="react-file-line html-div" data-testid="code-cell" data-line-number="282" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> check</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC283" class="react-file-line html-div" data-testid="code-cell" data-line-number="283" style="position:relative"> <span class="pl-k">die</span>(<span class="pl-s"><span class="pl-pds">"</span>ERROR: Failed to parse AUTO string - must contain any of a (API), l (FAIDX/htslib), c (cache), f (FASTA), p (plugins)<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>) <span class="pl-k">unless</span> <span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>^[alcfp]+<span class="pl-k">$</span><span class="pl-pds">/<span class="pl-k">i</span></span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC284" class="react-file-line html-div" data-testid="code-cell" data-line-number="284" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC285" class="react-file-line html-div" data-testid="code-cell" data-line-number="285" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> require species</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC286" class="react-file-line html-div" data-testid="code-cell" data-line-number="286" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>[cf]<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC287" class="react-file-line html-div" data-testid="code-cell" data-line-number="287" style="position:relative"> <span class="pl-k">die</span>(<span class="pl-s"><span class="pl-pds">"</span>ERROR: No species specified<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>) <span class="pl-k">unless</span> <span class="pl-smi">$SPECIES</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC288" class="react-file-line html-div" data-testid="code-cell" data-line-number="288" style="position:relative"> <span class="pl-smi">$SPECIES</span> = [<span class="pl-c1">split</span> /\,/, <span class="pl-smi">$SPECIES</span>];</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC289" class="react-file-line html-div" data-testid="code-cell" data-line-number="289" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC290" class="react-file-line html-div" data-testid="code-cell" data-line-number="290" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC291" class="react-file-line html-div" data-testid="code-cell" data-line-number="291" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> require plugin list</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC292" class="react-file-line html-div" data-testid="code-cell" data-line-number="292" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>p<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC293" class="react-file-line html-div" data-testid="code-cell" data-line-number="293" style="position:relative"> <span class="pl-k">die</span>(<span class="pl-s"><span class="pl-pds">"</span>ERROR: No plugins specified<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>) <span class="pl-k">unless</span> <span class="pl-smi">$PLUGINS</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC294" class="react-file-line html-div" data-testid="code-cell" data-line-number="294" style="position:relative"> <span class="pl-smi">$PLUGINS</span> = [<span class="pl-c1">split</span> /\,/, <span class="pl-smi">$PLUGINS</span>];</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC295" class="react-file-line html-div" data-testid="code-cell" data-line-number="295" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC296" class="react-file-line html-div" data-testid="code-cell" data-line-number="296" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC297" class="react-file-line html-div" data-testid="code-cell" data-line-number="297" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> run subs</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC298" class="react-file-line html-div" data-testid="code-cell" data-line-number="298" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>l<span class="pl-pds">/</span></span> && <span class="pl-smi">$AUTO</span> !~ <span class="pl-sr"><span class="pl-pds">/</span>a<span class="pl-pds">/</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC299" class="react-file-line html-div" data-testid="code-cell" data-line-number="299" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$curdir</span> = getcwd;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC300" class="react-file-line html-div" data-testid="code-cell" data-line-number="300" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$curdir</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC301" class="react-file-line html-div" data-testid="code-cell" data-line-number="301" style="position:relative"> install_biodbhts();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC302" class="react-file-line html-div" data-testid="code-cell" data-line-number="302" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$curdir</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC303" class="react-file-line html-div" data-testid="code-cell" data-line-number="303" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC304" class="react-file-line html-div" data-testid="code-cell" data-line-number="304" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> remove Bio dir if empty</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC305" class="react-file-line html-div" data-testid="code-cell" data-line-number="305" style="position:relative"> <span class="pl-c1">opendir</span> DIR, <span class="pl-smi">$DEST_DIR</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC306" class="react-file-line html-div" data-testid="code-cell" data-line-number="306" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">@files</span> = <span class="pl-c1">grep</span> {!/^\./} <span class="pl-c1">readdir</span> DIR;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC307" class="react-file-line html-div" data-testid="code-cell" data-line-number="307" style="position:relative"> <span class="pl-c1">closedir</span> DIR;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC308" class="react-file-line html-div" data-testid="code-cell" data-line-number="308" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC309" class="react-file-line html-div" data-testid="code-cell" data-line-number="309" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-c1">scalar</span> <span class="pl-smi">@files</span> <= 1) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC310" class="react-file-line html-div" data-testid="code-cell" data-line-number="310" style="position:relative"> rmtree(<span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/<span class="pl-pds">'</span></span>.<span class="pl-smi">$files</span>[0]);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC311" class="react-file-line html-div" data-testid="code-cell" data-line-number="311" style="position:relative"> rmtree(<span class="pl-smi">$DEST_DIR</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC312" class="react-file-line html-div" data-testid="code-cell" data-line-number="312" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC313" class="react-file-line html-div" data-testid="code-cell" data-line-number="313" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC314" class="react-file-line html-div" data-testid="code-cell" data-line-number="314" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC315" class="react-file-line html-div" data-testid="code-cell" data-line-number="315" style="position:relative"> api() <span class="pl-k">if</span> <span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>a<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC316" class="react-file-line html-div" data-testid="code-cell" data-line-number="316" style="position:relative"> cache() <span class="pl-k">if</span> <span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>c<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC317" class="react-file-line html-div" data-testid="code-cell" data-line-number="317" style="position:relative"> fasta() <span class="pl-k">if</span> <span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>f<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC318" class="react-file-line html-div" data-testid="code-cell" data-line-number="318" style="position:relative"> plugins() <span class="pl-k">if</span> <span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>p<span class="pl-pds">/</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC319" class="react-file-line html-div" data-testid="code-cell" data-line-number="319" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC320" class="react-file-line html-div" data-testid="code-cell" data-line-number="320" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC321" class="react-file-line html-div" data-testid="code-cell" data-line-number="321" style="position:relative"><span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC322" class="react-file-line html-div" data-testid="code-cell" data-line-number="322" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$api_msg</span> = </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC323" class="react-file-line html-div" data-testid="code-cell" data-line-number="323" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span> - Install v<span class="pl-smi">$API_VERSION</span> of the Ensembl API for use by the VEP. <span class="pl-pds">"</span></span> .</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC324" class="react-file-line html-div" data-testid="code-cell" data-line-number="324" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>It will not affect any existing installations of the Ensembl API that you may have.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC325" class="react-file-line html-div" data-testid="code-cell" data-line-number="325" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC326" class="react-file-line html-div" data-testid="code-cell" data-line-number="326" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Hello! This installer will help you set up VEP v<span class="pl-smi">$API_VERSION</span>, including:<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> .</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC327" class="react-file-line html-div" data-testid="code-cell" data-line-number="327" style="position:relative"> (<span class="pl-smi">$NO_UPDATE</span> ? <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> : <span class="pl-smi">$api_msg</span>) .</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC328" class="react-file-line html-div" data-testid="code-cell" data-line-number="328" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span> - Download and install cache files from Ensembl's FTP server.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> .</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC329" class="react-file-line html-div" data-testid="code-cell" data-line-number="329" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span> - Download FASTA files from Ensembl's FTP server.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> .</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC330" class="react-file-line html-div" data-testid="code-cell" data-line-number="330" style="position:relative"> (<span class="pl-smi">$NO_PLUGINS</span> ? <span class="pl-s"><span class="pl-pds">"</span><span class="pl-pds">"</span></span> : <span class="pl-s"><span class="pl-pds">"</span> - Download VEP plugins.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>) . <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC331" class="react-file-line html-div" data-testid="code-cell" data-line-number="331" style="position:relative"> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC332" class="react-file-line html-div" data-testid="code-cell" data-line-number="332" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC333" class="react-file-line html-div" data-testid="code-cell" data-line-number="333" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> run subs</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC334" class="react-file-line html-div" data-testid="code-cell" data-line-number="334" style="position:relative"> api() <span class="pl-k">if</span> check_api();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC335" class="react-file-line html-div" data-testid="code-cell" data-line-number="335" style="position:relative"> cache();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC336" class="react-file-line html-div" data-testid="code-cell" data-line-number="336" style="position:relative"> fasta();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC337" class="react-file-line html-div" data-testid="code-cell" data-line-number="337" style="position:relative"> plugins() <span class="pl-k">unless</span> <span class="pl-smi">$NO_PLUGINS</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC338" class="react-file-line html-div" data-testid="code-cell" data-line-number="338" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC339" class="react-file-line html-div" data-testid="code-cell" data-line-number="339" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC340" class="react-file-line html-div" data-testid="code-cell" data-line-number="340" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC341" class="react-file-line html-div" data-testid="code-cell" data-line-number="341" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> clean up</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC342" class="react-file-line html-div" data-testid="code-cell" data-line-number="342" style="position:relative"><span class="pl-k">if</span>(<span class="pl-k">-d</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$CACHE_DIR</span>/tmp<span class="pl-pds">"</span></span> && !<span class="pl-smi">$TEST</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC343" class="react-file-line html-div" data-testid="code-cell" data-line-number="343" style="position:relative"> rmtree(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$CACHE_DIR</span>/tmp<span class="pl-pds">"</span></span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not delete directory <span class="pl-smi">$CACHE_DIR</span>/tmp<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC344" class="react-file-line html-div" data-testid="code-cell" data-line-number="344" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC345" class="react-file-line html-div" data-testid="code-cell" data-line-number="345" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC346" class="react-file-line html-div" data-testid="code-cell" data-line-number="346" style="position:relative"><span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>All done<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC347" class="react-file-line html-div" data-testid="code-cell" data-line-number="347" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC348" class="react-file-line html-div" data-testid="code-cell" data-line-number="348" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC349" class="react-file-line html-div" data-testid="code-cell" data-line-number="349" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#########################################################################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC350" class="react-file-line html-div" data-testid="code-cell" data-line-number="350" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#########################################################################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC351" class="react-file-line html-div" data-testid="code-cell" data-line-number="351" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#########################################################################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC352" class="react-file-line html-div" data-testid="code-cell" data-line-number="352" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC353" class="react-file-line html-div" data-testid="code-cell" data-line-number="353" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC354" class="react-file-line html-div" data-testid="code-cell" data-line-number="354" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> UPDATE</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC355" class="react-file-line html-div" data-testid="code-cell" data-line-number="355" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#######</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC356" class="react-file-line html-div" data-testid="code-cell" data-line-number="356" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">update</span>() {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC357" class="react-file-line html-div" data-testid="code-cell" data-line-number="357" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC358" class="react-file-line html-div" data-testid="code-cell" data-line-number="358" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$module</span> = <span class="pl-smi">$VEP_MODULE_NAME</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC359" class="react-file-line html-div" data-testid="code-cell" data-line-number="359" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC360" class="react-file-line html-div" data-testid="code-cell" data-line-number="360" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> check for major version update</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC361" class="react-file-line html-div" data-testid="code-cell" data-line-number="361" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$repo_file</span> = <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$RealBin</span>/<span class="pl-smi">$$</span>.repo_file<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC362" class="react-file-line html-div" data-testid="code-cell" data-line-number="362" style="position:relative"> download_to_file(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC363" class="react-file-line html-div" data-testid="code-cell" data-line-number="363" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$git_api_root$module</span><span class="pl-pds">"</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC364" class="react-file-line html-div" data-testid="code-cell" data-line-number="364" style="position:relative"> <span class="pl-smi">$repo_file</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC365" class="react-file-line html-div" data-testid="code-cell" data-line-number="365" style="position:relative"> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC366" class="react-file-line html-div" data-testid="code-cell" data-line-number="366" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC367" class="react-file-line html-div" data-testid="code-cell" data-line-number="367" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$default_branch</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC368" class="react-file-line html-div" data-testid="code-cell" data-line-number="368" style="position:relative"> <span class="pl-c1">open</span> IN, <span class="pl-smi">$repo_file</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC369" class="react-file-line html-div" data-testid="code-cell" data-line-number="369" style="position:relative"> <span class="pl-k">while</span>(<IN>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC370" class="react-file-line html-div" data-testid="code-cell" data-line-number="370" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-sr"><span class="pl-pds">/</span>default_branch.+<span class="pl-cce">\:</span>.+<span class="pl-cce">\"</span>(.+?)<span class="pl-cce">\"</span><span class="pl-pds">/</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC371" class="react-file-line html-div" data-testid="code-cell" data-line-number="371" style="position:relative"> <span class="pl-smi">$default_branch</span> = <span class="pl-smi">$1</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC372" class="react-file-line html-div" data-testid="code-cell" data-line-number="372" style="position:relative"> <span class="pl-k">last</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC373" class="react-file-line html-div" data-testid="code-cell" data-line-number="373" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC374" class="react-file-line html-div" data-testid="code-cell" data-line-number="374" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC375" class="react-file-line html-div" data-testid="code-cell" data-line-number="375" style="position:relative"> <span class="pl-c1">close</span> IN;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC376" class="react-file-line html-div" data-testid="code-cell" data-line-number="376" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC377" class="react-file-line html-div" data-testid="code-cell" data-line-number="377" style="position:relative"> <span class="pl-c1">unlink</span>(<span class="pl-smi">$repo_file</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC378" class="react-file-line html-div" data-testid="code-cell" data-line-number="378" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC379" class="react-file-line html-div" data-testid="code-cell" data-line-number="379" style="position:relative"> <span class="pl-k">unless</span>(<span class="pl-smi">$default_branch</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC380" class="react-file-line html-div" data-testid="code-cell" data-line-number="380" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>WARNING: Unable to carry out version check for '<span class="pl-smi">$module</span>'<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC381" class="react-file-line html-div" data-testid="code-cell" data-line-number="381" style="position:relative"> <span class="pl-k">return</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC382" class="react-file-line html-div" data-testid="code-cell" data-line-number="382" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC383" class="react-file-line html-div" data-testid="code-cell" data-line-number="383" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC384" class="react-file-line html-div" data-testid="code-cell" data-line-number="384" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$default_branch_number</span> = <span class="pl-smi">$default_branch</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC385" class="react-file-line html-div" data-testid="code-cell" data-line-number="385" style="position:relative"> <span class="pl-smi">$default_branch_number</span> =~ <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">s</span>/</span>release<span class="pl-cce">\/</span></span><span class="pl-sr"><span class="pl-pds">//</span></span> <span class="pl-k">if</span> <span class="pl-smi">$default_branch_number</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC386" class="react-file-line html-div" data-testid="code-cell" data-line-number="386" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC387" class="react-file-line html-div" data-testid="code-cell" data-line-number="387" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$current_branch</span> = <span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-s"><span class="pl-pds">'</span>ensembl-vep<span class="pl-pds">'</span></span>}<span class="pl-k">-></span>{<span class="pl-c1">release</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC388" class="react-file-line html-div" data-testid="code-cell" data-line-number="388" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC389" class="react-file-line html-div" data-testid="code-cell" data-line-number="389" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$message</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC390" class="react-file-line html-div" data-testid="code-cell" data-line-number="390" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC391" class="react-file-line html-div" data-testid="code-cell" data-line-number="391" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> don't have latest</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC392" class="react-file-line html-div" data-testid="code-cell" data-line-number="392" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$current_branch</span> < <span class="pl-smi">$default_branch_number</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC393" class="react-file-line html-div" data-testid="code-cell" data-line-number="393" style="position:relative"> <span class="pl-smi">$message</span> = </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC394" class="react-file-line html-div" data-testid="code-cell" data-line-number="394" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>Version check reports a newer release of '<span class="pl-smi">$module</span>' is available <span class="pl-pds">"</span></span>.</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC395" class="react-file-line html-div" data-testid="code-cell" data-line-number="395" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>(installed: <span class="pl-smi">$current_branch</span>, available: <span class="pl-smi">$default_branch_number</span>)<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC396" class="react-file-line html-div" data-testid="code-cell" data-line-number="396" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC397" class="react-file-line html-div" data-testid="code-cell" data-line-number="397" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC398" class="react-file-line html-div" data-testid="code-cell" data-line-number="398" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> do have latest, but there might be updates</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC399" class="react-file-line html-div" data-testid="code-cell" data-line-number="399" style="position:relative"> <span class="pl-k">elsif</span>(<span class="pl-smi">$current_branch</span> == <span class="pl-smi">$default_branch_number</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC400" class="react-file-line html-div" data-testid="code-cell" data-line-number="400" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$git_sub</span> = get_vep_sub_version(<span class="pl-smi">$current_branch</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC401" class="react-file-line html-div" data-testid="code-cell" data-line-number="401" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$have_sub</span> = <span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>}<span class="pl-k">-></span>{<span class="pl-c1">sub</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC402" class="react-file-line html-div" data-testid="code-cell" data-line-number="402" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC403" class="react-file-line html-div" data-testid="code-cell" data-line-number="403" style="position:relative"> <span class="pl-smi">$message</span> = <span class="pl-c1">sprintf</span>(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC404" class="react-file-line html-div" data-testid="code-cell" data-line-number="404" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>Version check reports there are post-release updates available of <span class="pl-smi">%s</span> (installed: <span class="pl-smi">%s</span>.%.7s, available: <span class="pl-smi">%s</span>.%.7s)<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC405" class="react-file-line html-div" data-testid="code-cell" data-line-number="405" style="position:relative"> <span class="pl-smi">$module</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC406" class="react-file-line html-div" data-testid="code-cell" data-line-number="406" style="position:relative"> <span class="pl-smi">$current_branch</span>, <span class="pl-smi">$have_sub</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC407" class="react-file-line html-div" data-testid="code-cell" data-line-number="407" style="position:relative"> <span class="pl-smi">$current_branch</span>, <span class="pl-smi">$git_sub</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC408" class="react-file-line html-div" data-testid="code-cell" data-line-number="408" style="position:relative"> ) <span class="pl-k">unless</span> <span class="pl-smi">$git_sub</span> <span class="pl-c1">eq</span> <span class="pl-smi">$have_sub</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC409" class="react-file-line html-div" data-testid="code-cell" data-line-number="409" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC410" class="react-file-line html-div" data-testid="code-cell" data-line-number="410" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC411" class="react-file-line html-div" data-testid="code-cell" data-line-number="411" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$message</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC412" class="react-file-line html-div" data-testid="code-cell" data-line-number="412" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-smi">$message</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC413" class="react-file-line html-div" data-testid="code-cell" data-line-number="413" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC414" class="react-file-line html-div" data-testid="code-cell" data-line-number="414" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> user has git, suggest they use that instead</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC415" class="react-file-line html-div" data-testid="code-cell" data-line-number="415" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-s"><span class="pl-pds">`</span>which git<span class="pl-pds">`</span></span> && <span class="pl-k">-d</span> <span class="pl-smi">$RealBin</span>.<span class="pl-s"><span class="pl-pds">'</span>/.git<span class="pl-pds">'</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC416" class="react-file-line html-div" data-testid="code-cell" data-line-number="416" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>We recommend using git to update '<span class="pl-smi">$module</span>', by exiting this installer and running:<span class="pl-cce">\n\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC417" class="react-file-line html-div" data-testid="code-cell" data-line-number="417" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\t</span>git pull<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC418" class="react-file-line html-div" data-testid="code-cell" data-line-number="418" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\t</span>git checkout <span class="pl-smi">$default_branch</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">if</span> <span class="pl-smi">$current_branch</span> <span class="pl-c1">ne</span> <span class="pl-smi">$default_branch_number</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC419" class="react-file-line html-div" data-testid="code-cell" data-line-number="419" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC420" class="react-file-line html-div" data-testid="code-cell" data-line-number="420" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC421" class="react-file-line html-div" data-testid="code-cell" data-line-number="421" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>You should exit this installer and re-download '<span class="pl-smi">$module</span>' if you wish to update<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC422" class="react-file-line html-div" data-testid="code-cell" data-line-number="422" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC423" class="react-file-line html-div" data-testid="code-cell" data-line-number="423" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC424" class="react-file-line html-div" data-testid="code-cell" data-line-number="424" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>Do you wish to exit so you can get updates (y) or continue (n): <span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC425" class="react-file-line html-div" data-testid="code-cell" data-line-number="425" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC426" class="react-file-line html-div" data-testid="code-cell" data-line-number="426" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$ok</span> = <>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC427" class="react-file-line html-div" data-testid="code-cell" data-line-number="427" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC428" class="react-file-line html-div" data-testid="code-cell" data-line-number="428" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$ok</span> !~ <span class="pl-sr"><span class="pl-pds">/</span>^n<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC429" class="react-file-line html-div" data-testid="code-cell" data-line-number="429" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>OK, bye!<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC430" class="react-file-line html-div" data-testid="code-cell" data-line-number="430" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>NB: Remember to re-run INSTALL.pl after updating to check for API updates<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC431" class="react-file-line html-div" data-testid="code-cell" data-line-number="431" style="position:relative"> <span class="pl-k">exit</span>(0);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC432" class="react-file-line html-div" data-testid="code-cell" data-line-number="432" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC433" class="react-file-line html-div" data-testid="code-cell" data-line-number="433" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC434" class="react-file-line html-div" data-testid="code-cell" data-line-number="434" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC435" class="react-file-line html-div" data-testid="code-cell" data-line-number="435" style="position:relative"> <span class="pl-k">return</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC436" class="react-file-line html-div" data-testid="code-cell" data-line-number="436" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC437" class="react-file-line html-div" data-testid="code-cell" data-line-number="437" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC438" class="react-file-line html-div" data-testid="code-cell" data-line-number="438" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC439" class="react-file-line html-div" data-testid="code-cell" data-line-number="439" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC440" class="react-file-line html-div" data-testid="code-cell" data-line-number="440" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> CHECKS DIR SETUP AND PATHS ETC</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC441" class="react-file-line html-div" data-testid="code-cell" data-line-number="441" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>###############################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC442" class="react-file-line html-div" data-testid="code-cell" data-line-number="442" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC443" class="react-file-line html-div" data-testid="code-cell" data-line-number="443" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">is_url</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC444" class="react-file-line html-div" data-testid="code-cell" data-line-number="444" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$url</span> = <span class="pl-c1">shift</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC445" class="react-file-line html-div" data-testid="code-cell" data-line-number="445" style="position:relative"> <span class="pl-k">return</span> <span class="pl-smi">$url</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>^(http|ftp)<span class="pl-pds">/<span class="pl-k">i</span></span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC446" class="react-file-line html-div" data-testid="code-cell" data-line-number="446" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC447" class="react-file-line html-div" data-testid="code-cell" data-line-number="447" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC448" class="react-file-line html-div" data-testid="code-cell" data-line-number="448" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">check_default_dir</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC449" class="react-file-line html-div" data-testid="code-cell" data-line-number="449" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$this_os</span> = $^O;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC450" class="react-file-line html-div" data-testid="code-cell" data-line-number="450" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$default_dir_used</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC451" class="react-file-line html-div" data-testid="code-cell" data-line-number="451" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> check if $DEST_DIR is default</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC452" class="react-file-line html-div" data-testid="code-cell" data-line-number="452" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-c1">defined</span>(<span class="pl-smi">$DEST_DIR</span>)) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC453" class="react-file-line html-div" data-testid="code-cell" data-line-number="453" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Using non-default API installation directory <span class="pl-smi">$DEST_DIR</span>.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC454" class="react-file-line html-div" data-testid="code-cell" data-line-number="454" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Please note this just specifies the location for downloaded API files. The vep script will remain in its current location where ensembl-vep was unzipped.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC455" class="react-file-line html-div" data-testid="code-cell" data-line-number="455" style="position:relative"> <span class="pl-k">if</span>(!<span class="pl-c1">defined</span>(<span class="pl-smi">$AUTO</span>)){</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC456" class="react-file-line html-div" data-testid="code-cell" data-line-number="456" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Have you <span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC457" class="react-file-line html-div" data-testid="code-cell" data-line-number="457" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>1. added <span class="pl-smi">$DEST_DIR</span> to your PERL5LIB environment variable?<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC458" class="react-file-line html-div" data-testid="code-cell" data-line-number="458" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>2. added <span class="pl-smi">$DEST_DIR</span>/htslib to your PATH environment variable?<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC459" class="react-file-line html-div" data-testid="code-cell" data-line-number="459" style="position:relative"> <span class="pl-k">if</span>( <span class="pl-smi">$this_os</span> <span class="pl-c1">eq</span> <span class="pl-s"><span class="pl-pds">'</span>darwin<span class="pl-pds">'</span></span> && !<span class="pl-smi">$NO_HTSLIB</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC460" class="react-file-line html-div" data-testid="code-cell" data-line-number="460" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>3. added <span class="pl-smi">$DEST_DIR</span>/htslib to your DYLD_LIBRARY_PATH environment variable?<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC461" class="react-file-line html-div" data-testid="code-cell" data-line-number="461" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC462" class="react-file-line html-div" data-testid="code-cell" data-line-number="462" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>(y/n): <span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC463" class="react-file-line html-div" data-testid="code-cell" data-line-number="463" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC464" class="react-file-line html-div" data-testid="code-cell" data-line-number="464" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$ok</span> = <>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC465" class="react-file-line html-div" data-testid="code-cell" data-line-number="465" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$ok</span> !~ <span class="pl-sr"><span class="pl-pds">/</span>^y<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC466" class="react-file-line html-div" data-testid="code-cell" data-line-number="466" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Exiting. Please <span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC467" class="react-file-line html-div" data-testid="code-cell" data-line-number="467" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>1. add <span class="pl-smi">$DEST_DIR</span> to your PERL5LIB environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC468" class="react-file-line html-div" data-testid="code-cell" data-line-number="468" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>2. add <span class="pl-smi">$DEST_DIR</span>/htslib to your PATH environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC469" class="react-file-line html-div" data-testid="code-cell" data-line-number="469" style="position:relative"> <span class="pl-k">if</span>( <span class="pl-smi">$this_os</span> <span class="pl-c1">eq</span> <span class="pl-s"><span class="pl-pds">'</span>darwin<span class="pl-pds">'</span></span> && !<span class="pl-smi">$NO_HTSLIB</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC470" class="react-file-line html-div" data-testid="code-cell" data-line-number="470" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>3. add <span class="pl-smi">$DEST_DIR</span>/htslib to your DYLD_LIBRARY_PATH environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC471" class="react-file-line html-div" data-testid="code-cell" data-line-number="471" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC472" class="react-file-line html-div" data-testid="code-cell" data-line-number="472" style="position:relative"> <span class="pl-k">exit</span>(0);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC473" class="react-file-line html-div" data-testid="code-cell" data-line-number="473" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC474" class="react-file-line html-div" data-testid="code-cell" data-line-number="474" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC475" class="react-file-line html-div" data-testid="code-cell" data-line-number="475" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC476" class="react-file-line html-div" data-testid="code-cell" data-line-number="476" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<span class="pl-cce">\n\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC477" class="react-file-line html-div" data-testid="code-cell" data-line-number="477" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>PLEASE REMEMBER TO <span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC478" class="react-file-line html-div" data-testid="code-cell" data-line-number="478" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>1. add <span class="pl-smi">$DEST_DIR</span> to your PERL5LIB environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC479" class="react-file-line html-div" data-testid="code-cell" data-line-number="479" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>2. add <span class="pl-smi">$DEST_DIR</span>/htslib to your PATH environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC480" class="react-file-line html-div" data-testid="code-cell" data-line-number="480" style="position:relative"> <span class="pl-k">if</span>( <span class="pl-smi">$this_os</span> <span class="pl-c1">eq</span> <span class="pl-s"><span class="pl-pds">'</span>darwin<span class="pl-pds">'</span></span> && !<span class="pl-smi">$NO_HTSLIB</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC481" class="react-file-line html-div" data-testid="code-cell" data-line-number="481" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>3. add <span class="pl-smi">$DEST_DIR</span>/htslib to your DYLD_LIBRARY_PATH environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC482" class="react-file-line html-div" data-testid="code-cell" data-line-number="482" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC483" class="react-file-line html-div" data-testid="code-cell" data-line-number="483" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC484" class="react-file-line html-div" data-testid="code-cell" data-line-number="484" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC485" class="react-file-line html-div" data-testid="code-cell" data-line-number="485" style="position:relative"> <span class="pl-k">if</span>( ! <span class="pl-k">-d</span> <span class="pl-smi">$DEST_DIR</span> ) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC486" class="react-file-line html-div" data-testid="code-cell" data-line-number="486" style="position:relative"> <span class="pl-c1">mkdir</span> <span class="pl-smi">$DEST_DIR</span> || <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>Could not make destination directory <span class="pl-smi">$DEST_DIR</span><span class="pl-pds">"</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC487" class="react-file-line html-div" data-testid="code-cell" data-line-number="487" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC488" class="react-file-line html-div" data-testid="code-cell" data-line-number="488" style="position:relative"> <span class="pl-smi">$default_dir_used</span> = 0;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC489" class="react-file-line html-div" data-testid="code-cell" data-line-number="489" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC490" class="react-file-line html-div" data-testid="code-cell" data-line-number="490" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC491" class="react-file-line html-div" data-testid="code-cell" data-line-number="491" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC492" class="react-file-line html-div" data-testid="code-cell" data-line-number="492" style="position:relative"> <span class="pl-smi">$DEST_DIR</span> ||= <span class="pl-s"><span class="pl-pds">'</span>.<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC493" class="react-file-line html-div" data-testid="code-cell" data-line-number="493" style="position:relative"> <span class="pl-smi">$default_dir_used</span> = 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC494" class="react-file-line html-div" data-testid="code-cell" data-line-number="494" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$current_dir</span> = cwd();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC495" class="react-file-line html-div" data-testid="code-cell" data-line-number="495" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC496" class="react-file-line html-div" data-testid="code-cell" data-line-number="496" style="position:relative"> <span class="pl-k">if</span>( !<span class="pl-smi">$NO_HTSLIB</span> && <span class="pl-smi">$this_os</span> <span class="pl-c1">eq</span> <span class="pl-s"><span class="pl-pds">'</span>darwin<span class="pl-pds">'</span></span> ) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC497" class="react-file-line html-div" data-testid="code-cell" data-line-number="497" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Installation on OSX requires that you set up some paths before running this installer.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC498" class="react-file-line html-div" data-testid="code-cell" data-line-number="498" style="position:relative"> <span class="pl-k">if</span>(!<span class="pl-c1">defined</span>(<span class="pl-smi">$AUTO</span>)){</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC499" class="react-file-line html-div" data-testid="code-cell" data-line-number="499" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Have you <span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC500" class="react-file-line html-div" data-testid="code-cell" data-line-number="500" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>1. added <span class="pl-smi">$current_dir</span>/htslib to your DYLD_LIBRARY_PATH environment variable?<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC501" class="react-file-line html-div" data-testid="code-cell" data-line-number="501" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>(y/n): <span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC502" class="react-file-line html-div" data-testid="code-cell" data-line-number="502" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$ok</span> = <>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC503" class="react-file-line html-div" data-testid="code-cell" data-line-number="503" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$ok</span> !~ <span class="pl-sr"><span class="pl-pds">/</span>^y<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC504" class="react-file-line html-div" data-testid="code-cell" data-line-number="504" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Exiting. Please <span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC505" class="react-file-line html-div" data-testid="code-cell" data-line-number="505" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>1. add <span class="pl-smi">$current_dir</span>/htslib to your DYLD_LIBRARY_PATH environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC506" class="react-file-line html-div" data-testid="code-cell" data-line-number="506" style="position:relative"> <span class="pl-k">exit</span>(0);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC507" class="react-file-line html-div" data-testid="code-cell" data-line-number="507" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC508" class="react-file-line html-div" data-testid="code-cell" data-line-number="508" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC509" class="react-file-line html-div" data-testid="code-cell" data-line-number="509" style="position:relative"> <span class="pl-k">else</span>{</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC510" class="react-file-line html-div" data-testid="code-cell" data-line-number="510" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC511" class="react-file-line html-div" data-testid="code-cell" data-line-number="511" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span>print "\nPLEASE REMEMBER TO ADD $current_dir/htslib TO YOUR DYLD_LIBRARY_PATH ENVIRONMENT VARIABLE\n";</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC512" class="react-file-line html-div" data-testid="code-cell" data-line-number="512" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>PLEASE REMEMBER TO <span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC513" class="react-file-line html-div" data-testid="code-cell" data-line-number="513" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>1. add <span class="pl-smi">$current_dir</span>/htslib to your DYLD_LIBRARY_PATH environment variable<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC514" class="react-file-line html-div" data-testid="code-cell" data-line-number="514" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC515" class="react-file-line html-div" data-testid="code-cell" data-line-number="515" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC516" class="react-file-line html-div" data-testid="code-cell" data-line-number="516" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC517" class="react-file-line html-div" data-testid="code-cell" data-line-number="517" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC518" class="react-file-line html-div" data-testid="code-cell" data-line-number="518" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC519" class="react-file-line html-div" data-testid="code-cell" data-line-number="519" style="position:relative"> <span class="pl-k">return</span> <span class="pl-smi">$default_dir_used</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC520" class="react-file-line html-div" data-testid="code-cell" data-line-number="520" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC521" class="react-file-line html-div" data-testid="code-cell" data-line-number="521" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC522" class="react-file-line html-div" data-testid="code-cell" data-line-number="522" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC523" class="react-file-line html-div" data-testid="code-cell" data-line-number="523" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> API</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC524" class="react-file-line html-div" data-testid="code-cell" data-line-number="524" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>####</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC525" class="react-file-line html-div" data-testid="code-cell" data-line-number="525" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">api</span>() {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC526" class="react-file-line html-div" data-testid="code-cell" data-line-number="526" style="position:relative"> setup_dirs();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC527" class="react-file-line html-div" data-testid="code-cell" data-line-number="527" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$curdir</span> = getcwd;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC528" class="react-file-line html-div" data-testid="code-cell" data-line-number="528" style="position:relative"> <span class="pl-k">unless</span>(<span class="pl-smi">$NO_BIOPERL</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC529" class="react-file-line html-div" data-testid="code-cell" data-line-number="529" style="position:relative"> bioperl();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC530" class="react-file-line html-div" data-testid="code-cell" data-line-number="530" style="position:relative"> } </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC531" class="react-file-line html-div" data-testid="code-cell" data-line-number="531" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC532" class="react-file-line html-div" data-testid="code-cell" data-line-number="532" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> htslib needs to find bioperl to pass tests</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC533" class="react-file-line html-div" data-testid="code-cell" data-line-number="533" style="position:relative"> <span class="pl-smi">$ENV</span>{<span class="pl-c1">PERL5LIB</span>} = <span class="pl-smi">$ENV</span>{<span class="pl-c1">PERL5LIB</span>} ? <span class="pl-smi">$ENV</span>{<span class="pl-c1">PERL5LIB</span>}.<span class="pl-s"><span class="pl-pds">'</span>:<span class="pl-pds">'</span></span>.<span class="pl-smi">$DEST_DIR</span> : <span class="pl-smi">$DEST_DIR</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC534" class="react-file-line html-div" data-testid="code-cell" data-line-number="534" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC535" class="react-file-line html-div" data-testid="code-cell" data-line-number="535" style="position:relative"> <span class="pl-k">unless</span>(<span class="pl-smi">$NO_HTSLIB</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC536" class="react-file-line html-div" data-testid="code-cell" data-line-number="536" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$curdir</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC537" class="react-file-line html-div" data-testid="code-cell" data-line-number="537" style="position:relative"> install_biodbhts();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC538" class="react-file-line html-div" data-testid="code-cell" data-line-number="538" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC539" class="react-file-line html-div" data-testid="code-cell" data-line-number="539" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC540" class="react-file-line html-div" data-testid="code-cell" data-line-number="540" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$curdir</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC541" class="react-file-line html-div" data-testid="code-cell" data-line-number="541" style="position:relative"> install_api();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC542" class="react-file-line html-div" data-testid="code-cell" data-line-number="542" style="position:relative"> test() <span class="pl-k">unless</span> <span class="pl-smi">$NO_TEST</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC543" class="react-file-line html-div" data-testid="code-cell" data-line-number="543" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC544" class="react-file-line html-div" data-testid="code-cell" data-line-number="544" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC545" class="react-file-line html-div" data-testid="code-cell" data-line-number="545" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC546" class="react-file-line html-div" data-testid="code-cell" data-line-number="546" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> CHECK EXISTING</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC547" class="react-file-line html-div" data-testid="code-cell" data-line-number="547" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>###############</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC548" class="react-file-line html-div" data-testid="code-cell" data-line-number="548" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">check_api</span>() {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC549" class="react-file-line html-div" data-testid="code-cell" data-line-number="549" style="position:relative"> <span class="pl-k">return</span> 0 <span class="pl-k">if</span> <span class="pl-smi">$NO_UPDATE</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC550" class="react-file-line html-div" data-testid="code-cell" data-line-number="550" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Checking for installed versions of the Ensembl API...<span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC551" class="react-file-line html-div" data-testid="code-cell" data-line-number="551" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC552" class="react-file-line html-div" data-testid="code-cell" data-line-number="552" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$has_api</span> = {};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC553" class="react-file-line html-div" data-testid="code-cell" data-line-number="553" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$updates</span> = {};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC554" class="react-file-line html-div" data-testid="code-cell" data-line-number="554" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$core_version</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC555" class="react-file-line html-div" data-testid="code-cell" data-line-number="555" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">@unknown_versions</span> = ();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC556" class="react-file-line html-div" data-testid="code-cell" data-line-number="556" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC557" class="react-file-line html-div" data-testid="code-cell" data-line-number="557" style="position:relative"> <span class="pl-k">foreach</span> <span class="pl-k">my</span> <span class="pl-smi">$module_hash</span>(<span class="pl-smi">@API_MODULES</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC558" class="react-file-line html-div" data-testid="code-cell" data-line-number="558" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC559" class="react-file-line html-div" data-testid="code-cell" data-line-number="559" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$module</span> = <span class="pl-smi">$module_hash</span><span class="pl-k">-></span>{<span class="pl-c1">name</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC560" class="react-file-line html-div" data-testid="code-cell" data-line-number="560" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$test_pm</span> = <span class="pl-smi">$module_hash</span><span class="pl-k">-></span>{<span class="pl-c1">test_pm</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC561" class="react-file-line html-div" data-testid="code-cell" data-line-number="561" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC562" class="react-file-line html-div" data-testid="code-cell" data-line-number="562" style="position:relative"> <span class="pl-k">eval</span> <span class="pl-s"><span class="pl-pds">"</span>require <span class="pl-smi">$test_pm</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC563" class="react-file-line html-div" data-testid="code-cell" data-line-number="563" style="position:relative"> <span class="pl-smi">$has_api</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>} = <span class="pl-smi">$@</span> ? 0 : 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC564" class="react-file-line html-div" data-testid="code-cell" data-line-number="564" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC565" class="react-file-line html-div" data-testid="code-cell" data-line-number="565" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$has_api</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>}) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC566" class="react-file-line html-div" data-testid="code-cell" data-line-number="566" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$have_sub</span> = <span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>} ? (<span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>}<span class="pl-k">-></span>{<span class="pl-c1">sub</span>} || <span class="pl-s"><span class="pl-pds">'</span><span class="pl-pds">'</span></span>) : <span class="pl-s"><span class="pl-pds">'</span><span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC567" class="react-file-line html-div" data-testid="code-cell" data-line-number="567" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$git_sub</span> = get_module_sub_version(<span class="pl-smi">$module</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC568" class="react-file-line html-div" data-testid="code-cell" data-line-number="568" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC569" class="react-file-line html-div" data-testid="code-cell" data-line-number="569" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$have_sub</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC570" class="react-file-line html-div" data-testid="code-cell" data-line-number="570" style="position:relative"> <span class="pl-smi">$updates</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>} = [<span class="pl-smi">$have_sub</span>, <span class="pl-smi">$git_sub</span>] <span class="pl-k">if</span> <span class="pl-smi">$have_sub</span> <span class="pl-c1">ne</span> <span class="pl-smi">$git_sub</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC571" class="react-file-line html-div" data-testid="code-cell" data-line-number="571" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC572" class="react-file-line html-div" data-testid="code-cell" data-line-number="572" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC573" class="react-file-line html-div" data-testid="code-cell" data-line-number="573" style="position:relative"> <span class="pl-c1">push</span> <span class="pl-smi">@unknown_versions</span>, <span class="pl-smi">$module</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC574" class="react-file-line html-div" data-testid="code-cell" data-line-number="574" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC575" class="react-file-line html-div" data-testid="code-cell" data-line-number="575" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC576" class="react-file-line html-div" data-testid="code-cell" data-line-number="576" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$module</span> <span class="pl-c1">eq</span> <span class="pl-s"><span class="pl-pds">'</span>ensembl<span class="pl-pds">'</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC577" class="react-file-line html-div" data-testid="code-cell" data-line-number="577" style="position:relative"> <span class="pl-smi">$core_version</span> = Bio::EnsEMBL::Registry<span class="pl-k">-></span>software_version;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC578" class="react-file-line html-div" data-testid="code-cell" data-line-number="578" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC579" class="react-file-line html-div" data-testid="code-cell" data-line-number="579" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC580" class="react-file-line html-div" data-testid="code-cell" data-line-number="580" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC581" class="react-file-line html-div" data-testid="code-cell" data-line-number="581" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC582" class="react-file-line html-div" data-testid="code-cell" data-line-number="582" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>done<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC583" class="react-file-line html-div" data-testid="code-cell" data-line-number="583" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC584" class="react-file-line html-div" data-testid="code-cell" data-line-number="584" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$total</span> = 0;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC585" class="react-file-line html-div" data-testid="code-cell" data-line-number="585" style="position:relative"> <span class="pl-smi">$total</span> += <span class="pl-smi">$_</span> <span class="pl-k">for</span> <span class="pl-c1">values</span> <span class="pl-smi">%$has_api</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC586" class="react-file-line html-div" data-testid="code-cell" data-line-number="586" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC587" class="react-file-line html-div" data-testid="code-cell" data-line-number="587" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$message</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC588" class="react-file-line html-div" data-testid="code-cell" data-line-number="588" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC589" class="react-file-line html-div" data-testid="code-cell" data-line-number="589" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$total</span> == <span class="pl-c1">scalar</span> <span class="pl-smi">@API_MODULES</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC590" class="react-file-line html-div" data-testid="code-cell" data-line-number="590" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC591" class="react-file-line html-div" data-testid="code-cell" data-line-number="591" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-c1">defined</span>(<span class="pl-smi">$core_version</span>)) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC592" class="react-file-line html-div" data-testid="code-cell" data-line-number="592" style="position:relative"> <span class="pl-k">if</span>(!looks_like_number(<span class="pl-smi">$API_VERSION</span>)) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC593" class="react-file-line html-div" data-testid="code-cell" data-line-number="593" style="position:relative"> <span class="pl-smi">$message</span> = <span class="pl-s"><span class="pl-pds">"</span>Your reported version (<span class="pl-smi">$API_VERSION</span>) is a non-standard release number<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC594" class="react-file-line html-div" data-testid="code-cell" data-line-number="594" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC595" class="react-file-line html-div" data-testid="code-cell" data-line-number="595" style="position:relative"> <span class="pl-k">elsif</span>(<span class="pl-smi">$core_version</span> == <span class="pl-smi">$API_VERSION</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC596" class="react-file-line html-div" data-testid="code-cell" data-line-number="596" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC597" class="react-file-line html-div" data-testid="code-cell" data-line-number="597" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-c1">scalar</span> <span class="pl-c1">keys</span> <span class="pl-smi">%$updates</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC598" class="react-file-line html-div" data-testid="code-cell" data-line-number="598" style="position:relative"> <span class="pl-smi">$message</span> =</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC599" class="react-file-line html-div" data-testid="code-cell" data-line-number="599" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>There are updates available for these modules:<span class="pl-cce">\n</span> <span class="pl-pds">"</span></span>.</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC600" class="react-file-line html-div" data-testid="code-cell" data-line-number="600" style="position:relative"> <span class="pl-c1">join</span>(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC601" class="react-file-line html-div" data-testid="code-cell" data-line-number="601" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span> <span class="pl-pds">"</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC602" class="react-file-line html-div" data-testid="code-cell" data-line-number="602" style="position:relative"> <span class="pl-c1">map</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC603" class="react-file-line html-div" data-testid="code-cell" data-line-number="603" style="position:relative"> <span class="pl-c1">sprintf</span>(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC604" class="react-file-line html-div" data-testid="code-cell" data-line-number="604" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>%-20s : installed = %.7s, available = %.7s<span class="pl-pds">"</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC605" class="react-file-line html-div" data-testid="code-cell" data-line-number="605" style="position:relative"> <span class="pl-smi">$_</span>, <span class="pl-smi">$updates</span><span class="pl-k">-></span>{<span class="pl-smi">$_</span>}<span class="pl-k">-></span>[0], <span class="pl-smi">$updates</span><span class="pl-k">-></span>{<span class="pl-smi">$_</span>}<span class="pl-k">-></span>[1]</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC606" class="react-file-line html-div" data-testid="code-cell" data-line-number="606" style="position:relative"> )</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC607" class="react-file-line html-div" data-testid="code-cell" data-line-number="607" style="position:relative"> } <span class="pl-c1">keys</span> <span class="pl-smi">%$updates</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC608" class="react-file-line html-div" data-testid="code-cell" data-line-number="608" style="position:relative"> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC609" class="react-file-line html-div" data-testid="code-cell" data-line-number="609" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC610" class="react-file-line html-div" data-testid="code-cell" data-line-number="610" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC611" class="react-file-line html-div" data-testid="code-cell" data-line-number="611" style="position:relative"> <span class="pl-smi">$message</span> = <span class="pl-s"><span class="pl-pds">"</span>It looks like you already have v<span class="pl-smi">$API_VERSION</span> of the API installed.<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC612" class="react-file-line html-div" data-testid="code-cell" data-line-number="612" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC613" class="react-file-line html-div" data-testid="code-cell" data-line-number="613" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">@unknown_versions</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC614" class="react-file-line html-div" data-testid="code-cell" data-line-number="614" style="position:relative"> <span class="pl-smi">$message</span> .=</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC615" class="react-file-line html-div" data-testid="code-cell" data-line-number="615" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span>No version information was available for the following modules:<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>.</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC616" class="react-file-line html-div" data-testid="code-cell" data-line-number="616" style="position:relative"> <span class="pl-c1">join</span>(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>, <span class="pl-c1">map</span> {<span class="pl-s"><span class="pl-pds">"</span> - <span class="pl-pds">"</span></span>.<span class="pl-smi">$_</span>} <span class="pl-smi">@unknown_versions</span>).</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC617" class="react-file-line html-div" data-testid="code-cell" data-line-number="617" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>Updates may be available but you will need to perform these manually.<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC618" class="react-file-line html-div" data-testid="code-cell" data-line-number="618" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC619" class="react-file-line html-div" data-testid="code-cell" data-line-number="619" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC620" class="react-file-line html-div" data-testid="code-cell" data-line-number="620" style="position:relative"> <span class="pl-smi">$message</span> .= <span class="pl-s"><span class="pl-pds">"</span>You shouldn't need to install the API<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC621" class="react-file-line html-div" data-testid="code-cell" data-line-number="621" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC622" class="react-file-line html-div" data-testid="code-cell" data-line-number="622" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC623" class="react-file-line html-div" data-testid="code-cell" data-line-number="623" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC624" class="react-file-line html-div" data-testid="code-cell" data-line-number="624" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC625" class="react-file-line html-div" data-testid="code-cell" data-line-number="625" style="position:relative"> <span class="pl-k">elsif</span>(<span class="pl-smi">$core_version</span> > <span class="pl-smi">$API_VERSION</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC626" class="react-file-line html-div" data-testid="code-cell" data-line-number="626" style="position:relative"> <span class="pl-smi">$message</span> = <span class="pl-s"><span class="pl-pds">"</span>It looks like this installer is for an older distribution (<span class="pl-smi">$API_VERSION</span>) of the API than you already have (<span class="pl-smi">$core_version</span>)<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC627" class="react-file-line html-div" data-testid="code-cell" data-line-number="627" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC628" class="react-file-line html-div" data-testid="code-cell" data-line-number="628" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC629" class="react-file-line html-div" data-testid="code-cell" data-line-number="629" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC630" class="react-file-line html-div" data-testid="code-cell" data-line-number="630" style="position:relative"> <span class="pl-smi">$message</span> = <span class="pl-s"><span class="pl-pds">"</span>It looks like you have an older version (<span class="pl-smi">$core_version</span>) of the API installed.<span class="pl-cce">\n</span>This installer will install a limited set of the API v<span class="pl-smi">$API_VERSION</span> for use by the VEP only<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC631" class="react-file-line html-div" data-testid="code-cell" data-line-number="631" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC632" class="react-file-line html-div" data-testid="code-cell" data-line-number="632" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC633" class="react-file-line html-div" data-testid="code-cell" data-line-number="633" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC634" class="react-file-line html-div" data-testid="code-cell" data-line-number="634" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC635" class="react-file-line html-div" data-testid="code-cell" data-line-number="635" style="position:relative"> <span class="pl-smi">$message</span> = <span class="pl-s"><span class="pl-pds">"</span>It looks like you have an unidentified version of the API installed.<span class="pl-cce">\n</span>This installer will install a limited set of the API v<span class="pl-smi">$API_VERSION</span> for use by the VEP only<span class="pl-pds">"</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC636" class="react-file-line html-div" data-testid="code-cell" data-line-number="636" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC637" class="react-file-line html-div" data-testid="code-cell" data-line-number="637" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC638" class="react-file-line html-div" data-testid="code-cell" data-line-number="638" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC639" class="react-file-line html-div" data-testid="code-cell" data-line-number="639" style="position:relative"> <span class="pl-k">elsif</span>(<span class="pl-smi">$total</span> > 0) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC640" class="react-file-line html-div" data-testid="code-cell" data-line-number="640" style="position:relative"> <span class="pl-smi">$message</span> = <span class="pl-s"><span class="pl-pds">"</span>It looks like you already have the following API modules installed:<span class="pl-cce">\n\n</span><span class="pl-pds">"</span></span>.(<span class="pl-c1">join</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>, <span class="pl-c1">grep</span> {<span class="pl-smi">$has_api</span><span class="pl-k">-></span>{<span class="pl-smi">$_</span>}} <span class="pl-c1">keys</span> <span class="pl-smi">%$has_api</span>).<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n\n</span>Ensembl VEP requires the ensembl, ensembl-io, ensembl-variation, ensembl-compara and ensembl-funcgen modules<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC641" class="react-file-line html-div" data-testid="code-cell" data-line-number="641" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC642" class="react-file-line html-div" data-testid="code-cell" data-line-number="642" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC643" class="react-file-line html-div" data-testid="code-cell" data-line-number="643" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$AUTO</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>a<span class="pl-pds">/</span></span> || !<span class="pl-c1">defined</span>(<span class="pl-smi">$message</span>)) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC644" class="react-file-line html-div" data-testid="code-cell" data-line-number="644" style="position:relative"> <span class="pl-k">return</span> 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC645" class="react-file-line html-div" data-testid="code-cell" data-line-number="645" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC646" class="react-file-line html-div" data-testid="code-cell" data-line-number="646" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC647" class="react-file-line html-div" data-testid="code-cell" data-line-number="647" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-smi">$message</span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC648" class="react-file-line html-div" data-testid="code-cell" data-line-number="648" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC649" class="react-file-line html-div" data-testid="code-cell" data-line-number="649" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n\n</span>Skip to the next step (n) to install cache files<span class="pl-cce">\n\n</span>Do you want to continue installing the API (y/n)? <span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC650" class="react-file-line html-div" data-testid="code-cell" data-line-number="650" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$ok</span> = <>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC651" class="react-file-line html-div" data-testid="code-cell" data-line-number="651" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC652" class="react-file-line html-div" data-testid="code-cell" data-line-number="652" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$ok</span> !~ <span class="pl-sr"><span class="pl-pds">/</span>^y<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC653" class="react-file-line html-div" data-testid="code-cell" data-line-number="653" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span> - skipping API installation<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC654" class="react-file-line html-div" data-testid="code-cell" data-line-number="654" style="position:relative"> <span class="pl-k">return</span> 0;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC655" class="react-file-line html-div" data-testid="code-cell" data-line-number="655" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC656" class="react-file-line html-div" data-testid="code-cell" data-line-number="656" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC657" class="react-file-line html-div" data-testid="code-cell" data-line-number="657" style="position:relative"> <span class="pl-k">return</span> 1;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC658" class="react-file-line html-div" data-testid="code-cell" data-line-number="658" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC659" class="react-file-line html-div" data-testid="code-cell" data-line-number="659" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC660" class="react-file-line html-div" data-testid="code-cell" data-line-number="660" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC661" class="react-file-line html-div" data-testid="code-cell" data-line-number="661" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC662" class="react-file-line html-div" data-testid="code-cell" data-line-number="662" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC663" class="react-file-line html-div" data-testid="code-cell" data-line-number="663" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> SETUP</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC664" class="react-file-line html-div" data-testid="code-cell" data-line-number="664" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>######</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC665" class="react-file-line html-div" data-testid="code-cell" data-line-number="665" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">setup_dirs</span>() {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC666" class="react-file-line html-div" data-testid="code-cell" data-line-number="666" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC667" class="react-file-line html-div" data-testid="code-cell" data-line-number="667" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>Setting up directories<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC668" class="react-file-line html-div" data-testid="code-cell" data-line-number="668" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC669" class="react-file-line html-div" data-testid="code-cell" data-line-number="669" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> check if install dir exists</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC670" class="react-file-line html-div" data-testid="code-cell" data-line-number="670" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-k">-e</span> <span class="pl-smi">$DEST_DIR</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC671" class="react-file-line html-div" data-testid="code-cell" data-line-number="671" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$ok</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC672" class="react-file-line html-div" data-testid="code-cell" data-line-number="672" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC673" class="react-file-line html-div" data-testid="code-cell" data-line-number="673" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$AUTO</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC674" class="react-file-line html-div" data-testid="code-cell" data-line-number="674" style="position:relative"> <span class="pl-smi">$ok</span> = <span class="pl-s"><span class="pl-pds">'</span>y<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC675" class="react-file-line html-div" data-testid="code-cell" data-line-number="675" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC676" class="react-file-line html-div" data-testid="code-cell" data-line-number="676" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC677" class="react-file-line html-div" data-testid="code-cell" data-line-number="677" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Destination directory <span class="pl-smi">$DEST_DIR</span> already exists.<span class="pl-cce">\n</span>Do you want to overwrite it (if updating VEP this is probably OK) (y/n)? <span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC678" class="react-file-line html-div" data-testid="code-cell" data-line-number="678" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC679" class="react-file-line html-div" data-testid="code-cell" data-line-number="679" style="position:relative"> <span class="pl-smi">$ok</span> = <>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC680" class="react-file-line html-div" data-testid="code-cell" data-line-number="680" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC681" class="react-file-line html-div" data-testid="code-cell" data-line-number="681" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC682" class="react-file-line html-div" data-testid="code-cell" data-line-number="682" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$ok</span> !~ <span class="pl-sr"><span class="pl-pds">/</span>^y<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC683" class="react-file-line html-div" data-testid="code-cell" data-line-number="683" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Exiting<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC684" class="react-file-line html-div" data-testid="code-cell" data-line-number="684" style="position:relative"> <span class="pl-k">exit</span>(0);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC685" class="react-file-line html-div" data-testid="code-cell" data-line-number="685" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC686" class="react-file-line html-div" data-testid="code-cell" data-line-number="686" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC687" class="react-file-line html-div" data-testid="code-cell" data-line-number="687" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC688" class="react-file-line html-div" data-testid="code-cell" data-line-number="688" style="position:relative"> <span class="pl-k">unless</span>(<span class="pl-smi">$default_dir_used</span> || <span class="pl-smi">$AUTO</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC689" class="react-file-line html-div" data-testid="code-cell" data-line-number="689" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>WARNING: You are using a non-default install directory.<span class="pl-cce">\n</span>Pressing <span class="pl-cce">\"</span>y<span class="pl-cce">\"</span> again will remove <span class="pl-smi">$DEST_DIR</span> and its contents!!!<span class="pl-cce">\n</span>Are you really, really sure (y/n)? <span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC690" class="react-file-line html-div" data-testid="code-cell" data-line-number="690" style="position:relative"> <span class="pl-smi">$ok</span> = <>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC691" class="react-file-line html-div" data-testid="code-cell" data-line-number="691" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC692" class="react-file-line html-div" data-testid="code-cell" data-line-number="692" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-smi">$ok</span> !~ <span class="pl-sr"><span class="pl-pds">/</span>^y<span class="pl-pds">/<span class="pl-k">i</span></span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC693" class="react-file-line html-div" data-testid="code-cell" data-line-number="693" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Exiting<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC694" class="react-file-line html-div" data-testid="code-cell" data-line-number="694" style="position:relative"> <span class="pl-k">exit</span>(0);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC695" class="react-file-line html-div" data-testid="code-cell" data-line-number="695" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC696" class="react-file-line html-div" data-testid="code-cell" data-line-number="696" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC697" class="react-file-line html-div" data-testid="code-cell" data-line-number="697" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC698" class="react-file-line html-div" data-testid="code-cell" data-line-number="698" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> try to delete the existing dir</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC699" class="react-file-line html-div" data-testid="code-cell" data-line-number="699" style="position:relative"> rmtree(<span class="pl-smi">$DEST_DIR</span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not delete directory <span class="pl-smi">$DEST_DIR</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC700" class="react-file-line html-div" data-testid="code-cell" data-line-number="700" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC701" class="react-file-line html-div" data-testid="code-cell" data-line-number="701" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC702" class="react-file-line html-div" data-testid="code-cell" data-line-number="702" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC703" class="react-file-line html-div" data-testid="code-cell" data-line-number="703" style="position:relative"> <span class="pl-c1">mkdir</span>(<span class="pl-smi">$DEST_DIR</span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not make directory <span class="pl-smi">$DEST_DIR</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC704" class="react-file-line html-div" data-testid="code-cell" data-line-number="704" style="position:relative"> <span class="pl-c1">mkdir</span>(<span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/tmp<span class="pl-pds">'</span></span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not make directory <span class="pl-smi">$DEST_DIR</span>/tmp<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC705" class="react-file-line html-div" data-testid="code-cell" data-line-number="705" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC706" class="react-file-line html-div" data-testid="code-cell" data-line-number="706" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC707" class="react-file-line html-div" data-testid="code-cell" data-line-number="707" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC708" class="react-file-line html-div" data-testid="code-cell" data-line-number="708" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> INSTALL API</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC709" class="react-file-line html-div" data-testid="code-cell" data-line-number="709" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>############</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC710" class="react-file-line html-div" data-testid="code-cell" data-line-number="710" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">install_api</span>() {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC711" class="react-file-line html-div" data-testid="code-cell" data-line-number="711" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC712" class="react-file-line html-div" data-testid="code-cell" data-line-number="712" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span>Downloading required Ensembl API files<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC713" class="react-file-line html-div" data-testid="code-cell" data-line-number="713" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC714" class="react-file-line html-div" data-testid="code-cell" data-line-number="714" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$release_url_string</span> = looks_like_number(<span class="pl-smi">$API_VERSION</span>) ? <span class="pl-s"><span class="pl-pds">'</span>release/<span class="pl-pds">'</span></span>.<span class="pl-smi">$API_VERSION</span> : <span class="pl-smi">$API_VERSION</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC715" class="react-file-line html-div" data-testid="code-cell" data-line-number="715" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$release_path_string</span> = looks_like_number(<span class="pl-smi">$API_VERSION</span>) ? <span class="pl-s"><span class="pl-pds">'</span>release-<span class="pl-pds">'</span></span>.<span class="pl-smi">$API_VERSION</span> : <span class="pl-smi">$API_VERSION</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC716" class="react-file-line html-div" data-testid="code-cell" data-line-number="716" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC717" class="react-file-line html-div" data-testid="code-cell" data-line-number="717" style="position:relative"> <span class="pl-k">foreach</span> <span class="pl-k">my</span> <span class="pl-smi">$module_hash</span>(<span class="pl-smi">@API_MODULES</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC718" class="react-file-line html-div" data-testid="code-cell" data-line-number="718" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$module</span> = <span class="pl-smi">$module_hash</span><span class="pl-k">-></span>{<span class="pl-c1">name</span>};</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC719" class="react-file-line html-div" data-testid="code-cell" data-line-number="719" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC720" class="react-file-line html-div" data-testid="code-cell" data-line-number="720" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> do we need to update this?</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC721" class="react-file-line html-div" data-testid="code-cell" data-line-number="721" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$have_sub</span> = <span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>} ? (<span class="pl-smi">$CURRENT_VERSION_DATA</span><span class="pl-k">-></span>{<span class="pl-smi">$module</span>}<span class="pl-k">-></span>{<span class="pl-c1">sub</span>} || <span class="pl-s"><span class="pl-pds">'</span><span class="pl-pds">'</span></span>) : <span class="pl-s"><span class="pl-pds">'</span><span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC722" class="react-file-line html-div" data-testid="code-cell" data-line-number="722" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC723" class="react-file-line html-div" data-testid="code-cell" data-line-number="723" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$url</span> = <span class="pl-smi">$ENS_GIT_ROOT</span>.<span class="pl-smi">$module</span>.<span class="pl-smi">$ensembl_url_tail</span>.<span class="pl-smi">$release_url_string</span>.<span class="pl-smi">$archive_type</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC724" class="react-file-line html-div" data-testid="code-cell" data-line-number="724" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC725" class="react-file-line html-div" data-testid="code-cell" data-line-number="725" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span> - fetching <span class="pl-smi">$module</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC726" class="react-file-line html-div" data-testid="code-cell" data-line-number="726" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$target_file</span> = <span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/tmp/<span class="pl-pds">'</span></span>.<span class="pl-smi">$module</span>.<span class="pl-smi">$archive_type</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC727" class="react-file-line html-div" data-testid="code-cell" data-line-number="727" style="position:relative"> <span class="pl-c1">mkdir</span>(<span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/tmp/<span class="pl-pds">'</span></span>) <span class="pl-k">unless</span> <span class="pl-k">-d</span> <span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/tmp/<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC728" class="react-file-line html-div" data-testid="code-cell" data-line-number="728" style="position:relative"> download_to_file(<span class="pl-smi">$url</span>, <span class="pl-smi">$target_file</span>) <span class="pl-k">unless</span> <span class="pl-k">-e</span> <span class="pl-smi">$target_file</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC729" class="react-file-line html-div" data-testid="code-cell" data-line-number="729" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC730" class="react-file-line html-div" data-testid="code-cell" data-line-number="730" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span> - unpacking <span class="pl-smi">$target_file</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC731" class="react-file-line html-div" data-testid="code-cell" data-line-number="731" style="position:relative"> unpack_arch(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-smi">$module$archive_type</span><span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-pds">"</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC732" class="react-file-line html-div" data-testid="code-cell" data-line-number="732" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC733" class="react-file-line html-div" data-testid="code-cell" data-line-number="733" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span> - moving files<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC734" class="react-file-line html-div" data-testid="code-cell" data-line-number="734" style="position:relative"> <span class="pl-k">foreach</span> <span class="pl-k">my</span> <span class="pl-smi">$module_path</span> (<span class="pl-c1">split</span>(<span class="pl-s"><span class="pl-pds">'</span>,<span class="pl-pds">'</span></span>,<span class="pl-smi">$module_hash</span><span class="pl-k">-></span>{<span class="pl-c1">path</span>})) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC735" class="react-file-line html-div" data-testid="code-cell" data-line-number="735" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$module_dir_suffix</span> = <span class="pl-smi">$module_path</span> <span class="pl-c1">eq</span> <span class="pl-s"><span class="pl-pds">'</span> <span class="pl-pds">'</span></span> ? <span class="pl-s"><span class="pl-pds">'</span><span class="pl-pds">'</span></span> : <span class="pl-s"><span class="pl-pds">'</span>/<span class="pl-pds">'</span></span>.<span class="pl-smi">$module_path</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC736" class="react-file-line html-div" data-testid="code-cell" data-line-number="736" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$module_dir_from</span> = <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-smi">$module</span><span class="pl-cce">\-</span><span class="pl-smi">$release_path_string</span>/modules/Bio/EnsEMBL<span class="pl-smi">$module_dir_suffix</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC737" class="react-file-line html-div" data-testid="code-cell" data-line-number="737" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$module_dir_to</span> = <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/EnsEMBL<span class="pl-smi">$module_dir_suffix</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC738" class="react-file-line html-div" data-testid="code-cell" data-line-number="738" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC739" class="react-file-line html-div" data-testid="code-cell" data-line-number="739" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> If the target directory already exist, we can't overwrite it.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC740" class="react-file-line html-div" data-testid="code-cell" data-line-number="740" style="position:relative"> <span class="pl-k">if</span> (<span class="pl-k">-d</span> <span class="pl-smi">$module_dir_to</span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC741" class="react-file-line html-div" data-testid="code-cell" data-line-number="741" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> One solution is to move the content of the directory instead.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC742" class="react-file-line html-div" data-testid="code-cell" data-line-number="742" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> However we need to loop over the files/directories within the module directory because the 'move()' method doesn't allow wildcards.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC743" class="react-file-line html-div" data-testid="code-cell" data-line-number="743" style="position:relative"> <span class="pl-c1">opendir</span> DH, <span class="pl-smi">$module_dir_from</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC744" class="react-file-line html-div" data-testid="code-cell" data-line-number="744" style="position:relative"> <span class="pl-k">while</span>(<span class="pl-k">my</span> <span class="pl-smi">$file_or_dir</span> = <span class="pl-c1">readdir</span> DH) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC745" class="react-file-line html-div" data-testid="code-cell" data-line-number="745" style="position:relative"> <span class="pl-k">next</span> <span class="pl-k">if</span> (<span class="pl-smi">$file_or_dir</span> =~ <span class="pl-sr"><span class="pl-pds">/</span>^<span class="pl-cce">\.</span>+<span class="pl-k">$</span><span class="pl-pds">/</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC746" class="react-file-line html-div" data-testid="code-cell" data-line-number="746" style="position:relative"> move(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$module_dir_from</span>/<span class="pl-smi">$file_or_dir</span><span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$module_dir_to</span>/<span class="pl-smi">$file_or_dir</span><span class="pl-pds">"</span></span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not move '<span class="pl-smi">$module_dir_from</span>/<span class="pl-smi">$file_or_dir</span>'<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>.<span class="pl-smi">$!</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC747" class="react-file-line html-div" data-testid="code-cell" data-line-number="747" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC748" class="react-file-line html-div" data-testid="code-cell" data-line-number="748" style="position:relative"> <span class="pl-c1">closedir</span> DH;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC749" class="react-file-line html-div" data-testid="code-cell" data-line-number="749" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC750" class="react-file-line html-div" data-testid="code-cell" data-line-number="750" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC751" class="react-file-line html-div" data-testid="code-cell" data-line-number="751" style="position:relative"> move(<span class="pl-smi">$module_dir_from</span>, <span class="pl-smi">$module_dir_to</span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not move the directory '<span class="pl-smi">$module_dir_from</span>'<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>.<span class="pl-smi">$!</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC752" class="react-file-line html-div" data-testid="code-cell" data-line-number="752" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC753" class="react-file-line html-div" data-testid="code-cell" data-line-number="753" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC754" class="react-file-line html-div" data-testid="code-cell" data-line-number="754" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC755" class="react-file-line html-div" data-testid="code-cell" data-line-number="755" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> now get latest commit from github API</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC756" class="react-file-line html-div" data-testid="code-cell" data-line-number="756" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span> - getting version information<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC757" class="react-file-line html-div" data-testid="code-cell" data-line-number="757" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$git_sub</span> = get_module_sub_version(<span class="pl-smi">$module</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC758" class="react-file-line html-div" data-testid="code-cell" data-line-number="758" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC759" class="react-file-line html-div" data-testid="code-cell" data-line-number="759" style="position:relative"> <span class="pl-c1">mkdir</span>(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$RealBin</span>/.version/<span class="pl-pds">"</span></span>) <span class="pl-k">unless</span> <span class="pl-k">-d</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$RealBin</span>/.version/<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC760" class="react-file-line html-div" data-testid="code-cell" data-line-number="760" style="position:relative"> <span class="pl-c1">open</span> OUT, <span class="pl-s"><span class="pl-pds">"</span>><span class="pl-smi">$RealBin</span>/.version/<span class="pl-smi">$module</span><span class="pl-pds">"</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-smi">$!</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC761" class="react-file-line html-div" data-testid="code-cell" data-line-number="761" style="position:relative"> <span class="pl-c1">print</span> OUT <span class="pl-s"><span class="pl-pds">"</span>release <span class="pl-smi">$API_VERSION</span><span class="pl-cce">\n</span>sub <span class="pl-smi">$git_sub</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC762" class="react-file-line html-div" data-testid="code-cell" data-line-number="762" style="position:relative"> <span class="pl-c1">close</span> OUT;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC763" class="react-file-line html-div" data-testid="code-cell" data-line-number="763" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC764" class="react-file-line html-div" data-testid="code-cell" data-line-number="764" style="position:relative"> rmtree(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-smi">$module</span><span class="pl-cce">\-</span><span class="pl-smi">$release_path_string</span><span class="pl-pds">"</span></span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Failed to remove directory: <span class="pl-smi">$!</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC765" class="react-file-line html-div" data-testid="code-cell" data-line-number="765" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC766" class="react-file-line html-div" data-testid="code-cell" data-line-number="766" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC767" class="react-file-line html-div" data-testid="code-cell" data-line-number="767" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC768" class="react-file-line html-div" data-testid="code-cell" data-line-number="768" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">get_module_sub_version</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC769" class="react-file-line html-div" data-testid="code-cell" data-line-number="769" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$module</span> = <span class="pl-c1">shift</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC770" class="react-file-line html-div" data-testid="code-cell" data-line-number="770" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC771" class="react-file-line html-div" data-testid="code-cell" data-line-number="771" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$sub_file</span> = <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$RealBin</span>/<span class="pl-smi">$$</span><span class="pl-cce">\.</span><span class="pl-smi">$module</span>.sub<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC772" class="react-file-line html-div" data-testid="code-cell" data-line-number="772" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$release_url_string</span> = looks_like_number(<span class="pl-smi">$API_VERSION</span>) ? <span class="pl-s"><span class="pl-pds">'</span>release/<span class="pl-pds">'</span></span>.<span class="pl-smi">$API_VERSION</span> : <span class="pl-smi">$API_VERSION</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC773" class="react-file-line html-div" data-testid="code-cell" data-line-number="773" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC774" class="react-file-line html-div" data-testid="code-cell" data-line-number="774" style="position:relative"> download_to_file(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC775" class="react-file-line html-div" data-testid="code-cell" data-line-number="775" style="position:relative"> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$git_api_root$module</span>/commits?sha=<span class="pl-smi">$release_url_string</span><span class="pl-pds">"</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC776" class="react-file-line html-div" data-testid="code-cell" data-line-number="776" style="position:relative"> <span class="pl-smi">$sub_file</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC777" class="react-file-line html-div" data-testid="code-cell" data-line-number="777" style="position:relative"> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC778" class="react-file-line html-div" data-testid="code-cell" data-line-number="778" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC779" class="react-file-line html-div" data-testid="code-cell" data-line-number="779" style="position:relative"> <span class="pl-c1">open</span> IN, <span class="pl-smi">$sub_file</span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-smi">$!</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC780" class="react-file-line html-div" data-testid="code-cell" data-line-number="780" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$sub</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC781" class="react-file-line html-div" data-testid="code-cell" data-line-number="781" style="position:relative"> <span class="pl-k">while</span>(<IN>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC782" class="react-file-line html-div" data-testid="code-cell" data-line-number="782" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-sr"><span class="pl-pds">/</span><span class="pl-cce">\"</span>sha<span class="pl-cce">\"</span>: <span class="pl-cce">\"</span>(.+?)<span class="pl-cce">\"</span><span class="pl-pds">/</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC783" class="react-file-line html-div" data-testid="code-cell" data-line-number="783" style="position:relative"> <span class="pl-smi">$sub</span> = <span class="pl-smi">$1</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC784" class="react-file-line html-div" data-testid="code-cell" data-line-number="784" style="position:relative"> <span class="pl-k">last</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC785" class="react-file-line html-div" data-testid="code-cell" data-line-number="785" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC786" class="react-file-line html-div" data-testid="code-cell" data-line-number="786" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC787" class="react-file-line html-div" data-testid="code-cell" data-line-number="787" style="position:relative"> <span class="pl-c1">close</span> IN;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC788" class="react-file-line html-div" data-testid="code-cell" data-line-number="788" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC789" class="react-file-line html-div" data-testid="code-cell" data-line-number="789" style="position:relative"> <span class="pl-c1">unlink</span>(<span class="pl-smi">$sub_file</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC790" class="react-file-line html-div" data-testid="code-cell" data-line-number="790" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC791" class="react-file-line html-div" data-testid="code-cell" data-line-number="791" style="position:relative"> <span class="pl-k">return</span> <span class="pl-smi">$sub</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC792" class="react-file-line html-div" data-testid="code-cell" data-line-number="792" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC793" class="react-file-line html-div" data-testid="code-cell" data-line-number="793" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC794" class="react-file-line html-div" data-testid="code-cell" data-line-number="794" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">get_vep_sub_version</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC795" class="react-file-line html-div" data-testid="code-cell" data-line-number="795" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$release</span> = <span class="pl-c1">shift</span> || <span class="pl-smi">$API_VERSION</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC796" class="react-file-line html-div" data-testid="code-cell" data-line-number="796" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC797" class="react-file-line html-div" data-testid="code-cell" data-line-number="797" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$sub_file</span> = <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$RealBin</span>/<span class="pl-smi">$$</span><span class="pl-cce">\.</span><span class="pl-smi">$VEP_MODULE_NAME</span>.sub<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC798" class="react-file-line html-div" data-testid="code-cell" data-line-number="798" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$release_url_string</span> = looks_like_number(<span class="pl-smi">$release</span>) ? <span class="pl-s"><span class="pl-pds">'</span>release/<span class="pl-pds">'</span></span>.<span class="pl-smi">$release</span> : <span class="pl-smi">$release</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC799" class="react-file-line html-div" data-testid="code-cell" data-line-number="799" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC800" class="react-file-line html-div" data-testid="code-cell" data-line-number="800" style="position:relative"> download_to_file(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC801" class="react-file-line html-div" data-testid="code-cell" data-line-number="801" style="position:relative"> <span class="pl-c1">sprintf</span>(</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC802" class="react-file-line html-div" data-testid="code-cell" data-line-number="802" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>https://raw.githubusercontent.com/Ensembl/%s/%s/modules/Bio/EnsEMBL/VEP/Constants.pm<span class="pl-pds">'</span></span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC803" class="react-file-line html-div" data-testid="code-cell" data-line-number="803" style="position:relative"> <span class="pl-smi">$VEP_MODULE_NAME</span>,</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC804" class="react-file-line html-div" data-testid="code-cell" data-line-number="804" style="position:relative"> <span class="pl-smi">$release_url_string</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC805" class="react-file-line html-div" data-testid="code-cell" data-line-number="805" style="position:relative"> ),</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC806" class="react-file-line html-div" data-testid="code-cell" data-line-number="806" style="position:relative"> <span class="pl-smi">$sub_file</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC807" class="react-file-line html-div" data-testid="code-cell" data-line-number="807" style="position:relative"> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC808" class="react-file-line html-div" data-testid="code-cell" data-line-number="808" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC809" class="react-file-line html-div" data-testid="code-cell" data-line-number="809" style="position:relative"> <span class="pl-c1">open</span> IN, <span class="pl-smi">$sub_file</span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-smi">$!</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC810" class="react-file-line html-div" data-testid="code-cell" data-line-number="810" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$sub</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC811" class="react-file-line html-div" data-testid="code-cell" data-line-number="811" style="position:relative"> <span class="pl-k">while</span>(<IN>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC812" class="react-file-line html-div" data-testid="code-cell" data-line-number="812" style="position:relative"> <span class="pl-k">if</span>(<span class="pl-sr"><span class="pl-pds">/</span>VEP_SUB_VERSION <span class="pl-cce">\=</span> (.+)<span class="pl-cce">\;</span><span class="pl-pds">/</span></span>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC813" class="react-file-line html-div" data-testid="code-cell" data-line-number="813" style="position:relative"> <span class="pl-smi">$sub</span> = <span class="pl-smi">$1</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC814" class="react-file-line html-div" data-testid="code-cell" data-line-number="814" style="position:relative"> <span class="pl-k">last</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC815" class="react-file-line html-div" data-testid="code-cell" data-line-number="815" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC816" class="react-file-line html-div" data-testid="code-cell" data-line-number="816" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC817" class="react-file-line html-div" data-testid="code-cell" data-line-number="817" style="position:relative"> <span class="pl-c1">close</span> IN;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC818" class="react-file-line html-div" data-testid="code-cell" data-line-number="818" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC819" class="react-file-line html-div" data-testid="code-cell" data-line-number="819" style="position:relative"> <span class="pl-c1">unlink</span>(<span class="pl-smi">$sub_file</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC820" class="react-file-line html-div" data-testid="code-cell" data-line-number="820" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC821" class="react-file-line html-div" data-testid="code-cell" data-line-number="821" style="position:relative"> <span class="pl-k">return</span> <span class="pl-smi">$sub</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC822" class="react-file-line html-div" data-testid="code-cell" data-line-number="822" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC823" class="react-file-line html-div" data-testid="code-cell" data-line-number="823" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC824" class="react-file-line html-div" data-testid="code-cell" data-line-number="824" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> HTSLIB download/make</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC825" class="react-file-line html-div" data-testid="code-cell" data-line-number="825" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#####################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC826" class="react-file-line html-div" data-testid="code-cell" data-line-number="826" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">install_htslib</span>() {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC827" class="react-file-line html-div" data-testid="code-cell" data-line-number="827" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC828" class="react-file-line html-div" data-testid="code-cell" data-line-number="828" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span>actually decided to follow Bio::DB::Sam template</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC829" class="react-file-line html-div" data-testid="code-cell" data-line-number="829" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> STEP 0: various dependencies</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC830" class="react-file-line html-div" data-testid="code-cell" data-line-number="830" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$git</span> = <span class="pl-s"><span class="pl-pds">`</span>which git<span class="pl-pds">`</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC831" class="react-file-line html-div" data-testid="code-cell" data-line-number="831" style="position:relative"> <span class="pl-smi">$git</span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds"><<END</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC832" class="react-file-line html-div" data-testid="code-cell" data-line-number="832" style="position:relative"><span class="pl-s"> 'git' command not in path. Please install git and try again.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC833" class="react-file-line html-div" data-testid="code-cell" data-line-number="833" style="position:relative"><span class="pl-s"> (or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC834" class="react-file-line html-div" data-testid="code-cell" data-line-number="834" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC835" class="react-file-line html-div" data-testid="code-cell" data-line-number="835" style="position:relative"><span class="pl-s"> On Debian/Ubuntu systems you can do this with the command:</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC836" class="react-file-line html-div" data-testid="code-cell" data-line-number="836" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC837" class="react-file-line html-div" data-testid="code-cell" data-line-number="837" style="position:relative"><span class="pl-s"> apt-get install git</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC838" class="react-file-line html-div" data-testid="code-cell" data-line-number="838" style="position:relative"><span class="pl-s"><span class="pl-pds">END</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC839" class="react-file-line html-div" data-testid="code-cell" data-line-number="839" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC840" class="react-file-line html-div" data-testid="code-cell" data-line-number="840" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC841" class="react-file-line html-div" data-testid="code-cell" data-line-number="841" style="position:relative"> <span class="pl-s"><span class="pl-pds">`</span>which cc<span class="pl-pds">`</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds"><<END</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC842" class="react-file-line html-div" data-testid="code-cell" data-line-number="842" style="position:relative"><span class="pl-s"> 'cc' command not in path. Please install it and try again.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC843" class="react-file-line html-div" data-testid="code-cell" data-line-number="843" style="position:relative"><span class="pl-s"> (or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC844" class="react-file-line html-div" data-testid="code-cell" data-line-number="844" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC845" class="react-file-line html-div" data-testid="code-cell" data-line-number="845" style="position:relative"><span class="pl-s"> On Debian/Ubuntu systems you can do this with the command:</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC846" class="react-file-line html-div" data-testid="code-cell" data-line-number="846" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC847" class="react-file-line html-div" data-testid="code-cell" data-line-number="847" style="position:relative"><span class="pl-s"> apt-get install build-essential</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC848" class="react-file-line html-div" data-testid="code-cell" data-line-number="848" style="position:relative"><span class="pl-s"><span class="pl-pds">END</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC849" class="react-file-line html-div" data-testid="code-cell" data-line-number="849" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC850" class="react-file-line html-div" data-testid="code-cell" data-line-number="850" style="position:relative"> <span class="pl-s"><span class="pl-pds">`</span>which make<span class="pl-pds">`</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds"><<END</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC851" class="react-file-line html-div" data-testid="code-cell" data-line-number="851" style="position:relative"><span class="pl-s"> 'make' command not in path. Please install it and try again.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC852" class="react-file-line html-div" data-testid="code-cell" data-line-number="852" style="position:relative"><span class="pl-s"> (or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC853" class="react-file-line html-div" data-testid="code-cell" data-line-number="853" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC854" class="react-file-line html-div" data-testid="code-cell" data-line-number="854" style="position:relative"><span class="pl-s"> On Debian/Ubuntu systems you can do this with the command:</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC855" class="react-file-line html-div" data-testid="code-cell" data-line-number="855" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC856" class="react-file-line html-div" data-testid="code-cell" data-line-number="856" style="position:relative"><span class="pl-s"> apt-get install build-essential</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC857" class="react-file-line html-div" data-testid="code-cell" data-line-number="857" style="position:relative"><span class="pl-s"><span class="pl-pds">END</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC858" class="react-file-line html-div" data-testid="code-cell" data-line-number="858" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC859" class="react-file-line html-div" data-testid="code-cell" data-line-number="859" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> List the required libraries with their packages</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC860" class="react-file-line html-div" data-testid="code-cell" data-line-number="860" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">%libs</span> = ( </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC861" class="react-file-line html-div" data-testid="code-cell" data-line-number="861" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>zlib.h<span class="pl-pds">'</span></span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>zlib1g-dev<span class="pl-pds">'</span></span>, </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC862" class="react-file-line html-div" data-testid="code-cell" data-line-number="862" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>lzma.h<span class="pl-pds">'</span></span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>liblzma-dev<span class="pl-pds">'</span></span>, </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC863" class="react-file-line html-div" data-testid="code-cell" data-line-number="863" style="position:relative"> <span class="pl-s"><span class="pl-pds">'</span>bzlib.h<span class="pl-pds">'</span></span> <span class="pl-k">=></span> <span class="pl-s"><span class="pl-pds">'</span>libbz2-dev<span class="pl-pds">'</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC864" class="react-file-line html-div" data-testid="code-cell" data-line-number="864" style="position:relative"> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC865" class="react-file-line html-div" data-testid="code-cell" data-line-number="865" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC866" class="react-file-line html-div" data-testid="code-cell" data-line-number="866" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$msg</span> = <span class="pl-s"><span class="pl-pds">'</span><span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC867" class="react-file-line html-div" data-testid="code-cell" data-line-number="867" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$this_os</span> = $^O;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC868" class="react-file-line html-div" data-testid="code-cell" data-line-number="868" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC869" class="react-file-line html-div" data-testid="code-cell" data-line-number="869" style="position:relative"> <span class="pl-k">if</span> (<span class="pl-smi">$this_os</span> <span class="pl-c1">ne</span> <span class="pl-s"><span class="pl-pds">'</span>darwin<span class="pl-pds">'</span></span> ) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC870" class="react-file-line html-div" data-testid="code-cell" data-line-number="870" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC871" class="react-file-line html-div" data-testid="code-cell" data-line-number="871" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$default_msg</span> = <span class="pl-s"><span class="pl-pds">qq{</span><span class="pl-smi">%s</span> library header(s) not found in /usr/include. Please install it and try again.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC872" class="react-file-line html-div" data-testid="code-cell" data-line-number="872" style="position:relative"><span class="pl-s">(or to skip Bio::DB::HTS/htslib install re-run with --NO_HTSLIB)</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC873" class="react-file-line html-div" data-testid="code-cell" data-line-number="873" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC874" class="react-file-line html-div" data-testid="code-cell" data-line-number="874" style="position:relative"><span class="pl-s">On Debian/Ubuntu systems you can do this with the command:</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC875" class="react-file-line html-div" data-testid="code-cell" data-line-number="875" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC876" class="react-file-line html-div" data-testid="code-cell" data-line-number="876" style="position:relative"><span class="pl-s">apt-get install <span class="pl-smi">%s</span><span class="pl-pds">}</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC877" class="react-file-line html-div" data-testid="code-cell" data-line-number="877" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">@missing_header</span> = ();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC878" class="react-file-line html-div" data-testid="code-cell" data-line-number="878" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">@missing_library</span> = (); </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC879" class="react-file-line html-div" data-testid="code-cell" data-line-number="879" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> Loop over the required libraries</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC880" class="react-file-line html-div" data-testid="code-cell" data-line-number="880" style="position:relative"> <span class="pl-k">foreach</span> <span class="pl-k">my</span> <span class="pl-smi">$lib</span> (<span class="pl-c1">sort</span>(<span class="pl-c1">keys</span>(<span class="pl-smi">%libs</span>))) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC881" class="react-file-line html-div" data-testid="code-cell" data-line-number="881" style="position:relative"> <span class="pl-k">unless</span>(<span class="pl-k">-e</span> <span class="pl-s"><span class="pl-pds">'</span>/usr/include/<span class="pl-pds">'</span></span>.<span class="pl-smi">$lib</span>){</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC882" class="react-file-line html-div" data-testid="code-cell" data-line-number="882" style="position:relative"> <span class="pl-c1">push</span>(<span class="pl-smi">@missing_header</span>, <span class="pl-smi">$lib</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC883" class="react-file-line html-div" data-testid="code-cell" data-line-number="883" style="position:relative"> <span class="pl-c1">push</span>(<span class="pl-smi">@missing_library</span>, <span class="pl-smi">$libs</span>{<span class="pl-smi">$lib</span>});</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC884" class="react-file-line html-div" data-testid="code-cell" data-line-number="884" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC885" class="react-file-line html-div" data-testid="code-cell" data-line-number="885" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC886" class="react-file-line html-div" data-testid="code-cell" data-line-number="886" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$header_string</span> = <span class="pl-c1">join</span>( <span class="pl-s"><span class="pl-pds">'</span>, <span class="pl-pds">'</span></span>, <span class="pl-smi">@missing_header</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC887" class="react-file-line html-div" data-testid="code-cell" data-line-number="887" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$install_string</span> = <span class="pl-c1">join</span>( <span class="pl-s"><span class="pl-pds">'</span> <span class="pl-pds">'</span></span>, <span class="pl-smi">@missing_library</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC888" class="react-file-line html-div" data-testid="code-cell" data-line-number="888" style="position:relative"> <span class="pl-k">die</span>(<span class="pl-c1">sprintf</span>(<span class="pl-smi">$default_msg</span>, <span class="pl-smi">$header_string</span>, <span class="pl-smi">$install_string</span>). <span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n\n</span><span class="pl-pds">"</span></span>) <span class="pl-k">if</span>(<span class="pl-smi">$header_string</span> <span class="pl-c1">ne</span> <span class="pl-s"><span class="pl-pds">'</span><span class="pl-pds">'</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC889" class="react-file-line html-div" data-testid="code-cell" data-line-number="889" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC890" class="react-file-line html-div" data-testid="code-cell" data-line-number="890" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC891" class="react-file-line html-div" data-testid="code-cell" data-line-number="891" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> STEP 1: Create a clean directory for building</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC892" class="react-file-line html-div" data-testid="code-cell" data-line-number="892" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$htslib_install_dir</span> = <span class="pl-smi">$LIB_DIR</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC893" class="react-file-line html-div" data-testid="code-cell" data-line-number="893" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$curdir</span> = getcwd;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC894" class="react-file-line html-div" data-testid="code-cell" data-line-number="894" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$htslib_install_dir</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC895" class="react-file-line html-div" data-testid="code-cell" data-line-number="895" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$actualdir</span> = getcwd;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC896" class="react-file-line html-div" data-testid="code-cell" data-line-number="896" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC897" class="react-file-line html-div" data-testid="code-cell" data-line-number="897" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> STEP 2: Check out HTSLIB / or make this a download?</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC898" class="react-file-line html-div" data-testid="code-cell" data-line-number="898" style="position:relative"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span> - checking out HTSLib<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC899" class="react-file-line html-div" data-testid="code-cell" data-line-number="899" style="position:relative"> <span class="pl-c1">system</span> <span class="pl-s"><span class="pl-pds">"</span>git clone -b <span class="pl-smi">$HTSLIB_VERSION</span> https://github.com/samtools/htslib.git<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC900" class="react-file-line html-div" data-testid="code-cell" data-line-number="900" style="position:relative"> <span class="pl-k">-d</span> <span class="pl-s"><span class="pl-pds">'</span>./htslib<span class="pl-pds">'</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>git clone seems to have failed. Could not find <span class="pl-smi">$htslib_install_dir</span>/htslib directory<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC901" class="react-file-line html-div" data-testid="code-cell" data-line-number="901" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-s"><span class="pl-pds">'</span>./htslib<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC902" class="react-file-line html-div" data-testid="code-cell" data-line-number="902" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC903" class="react-file-line html-div" data-testid="code-cell" data-line-number="903" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> Step 3: Build libhts.a</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC904" class="react-file-line html-div" data-testid="code-cell" data-line-number="904" style="position:relative"> <span class="pl-c1">print</span>(<span class="pl-s"><span class="pl-pds">"</span> - building HTSLIB in <span class="pl-smi">$htslib_install_dir</span>/htslib<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC905" class="react-file-line html-div" data-testid="code-cell" data-line-number="905" style="position:relative"> <span class="pl-c1">print</span>( <span class="pl-s"><span class="pl-pds">"</span>In <span class="pl-pds">"</span></span>.getcwd.<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC906" class="react-file-line html-div" data-testid="code-cell" data-line-number="906" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> patch makefile</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC907" class="react-file-line html-div" data-testid="code-cell" data-line-number="907" style="position:relative"> <span class="pl-c1">rename</span> <span class="pl-s"><span class="pl-pds">'</span>Makefile<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>Makefile.orig<span class="pl-pds">'</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>Couldn't rename Makefile to Makefile.orig: <span class="pl-smi">$!</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC908" class="react-file-line html-div" data-testid="code-cell" data-line-number="908" style="position:relative"> <span class="pl-c1">open</span> <span class="pl-k">my</span> <span class="pl-smi">$in</span>, <span class="pl-s"><span class="pl-pds">'</span><<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>Makefile.orig<span class="pl-pds">'</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>Couldn't open Makefile for reading: <span class="pl-smi">$!</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC909" class="react-file-line html-div" data-testid="code-cell" data-line-number="909" style="position:relative"> <span class="pl-c1">open</span> <span class="pl-k">my</span> <span class="pl-smi">$out</span>,<span class="pl-s"><span class="pl-pds">'</span>><span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>Makefile.new<span class="pl-pds">'</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>Couldn't open Makefile.new for writing: <span class="pl-smi">$!</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC910" class="react-file-line html-div" data-testid="code-cell" data-line-number="910" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC911" class="react-file-line html-div" data-testid="code-cell" data-line-number="911" style="position:relative"> <span class="pl-k">while</span> (<<span class="pl-smi">$in</span>>) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC912" class="react-file-line html-div" data-testid="code-cell" data-line-number="912" style="position:relative"> <span class="pl-c1">chomp</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC913" class="react-file-line html-div" data-testid="code-cell" data-line-number="913" style="position:relative"> <span class="pl-k">if</span> (<span class="pl-sr"><span class="pl-pds">/</span>^CFLAGS<span class="pl-pds">/</span></span> && !/-fPIC/) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC914" class="react-file-line html-div" data-testid="code-cell" data-line-number="914" style="position:relative"> <span class="pl-sr"><span class="pl-pds"><span class="pl-c1">s</span>/</span>#.+</span><span class="pl-sr"><span class="pl-pds">//</span></span>; <span class="pl-c"><span class="pl-c">#</span> get rid of comments</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC915" class="react-file-line html-div" data-testid="code-cell" data-line-number="915" style="position:relative"> <span class="pl-smi">$_</span> .= <span class="pl-s"><span class="pl-pds">"</span> -fPIC -Wno-unused -Wno-unused-result<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC916" class="react-file-line html-div" data-testid="code-cell" data-line-number="916" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC917" class="react-file-line html-div" data-testid="code-cell" data-line-number="917" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC918" class="react-file-line html-div" data-testid="code-cell" data-line-number="918" style="position:relative"> <span class="pl-k">continue</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC919" class="react-file-line html-div" data-testid="code-cell" data-line-number="919" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-smi">$out</span> <span class="pl-smi">$_</span>,<span class="pl-s"><span class="pl-pds">"</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC920" class="react-file-line html-div" data-testid="code-cell" data-line-number="920" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC921" class="react-file-line html-div" data-testid="code-cell" data-line-number="921" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC922" class="react-file-line html-div" data-testid="code-cell" data-line-number="922" style="position:relative"> <span class="pl-c1">close</span> <span class="pl-smi">$in</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC923" class="react-file-line html-div" data-testid="code-cell" data-line-number="923" style="position:relative"> <span class="pl-c1">close</span> <span class="pl-smi">$out</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC924" class="react-file-line html-div" data-testid="code-cell" data-line-number="924" style="position:relative"> <span class="pl-c1">rename</span> <span class="pl-s"><span class="pl-pds">'</span>Makefile.new<span class="pl-pds">'</span></span>,<span class="pl-s"><span class="pl-pds">'</span>Makefile<span class="pl-pds">'</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>Couldn't rename Makefile.new to Makefile: <span class="pl-smi">$!</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC925" class="react-file-line html-div" data-testid="code-cell" data-line-number="925" style="position:relative"> <span class="pl-c1">system</span> <span class="pl-s"><span class="pl-pds">"</span>make<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC926" class="react-file-line html-div" data-testid="code-cell" data-line-number="926" style="position:relative"> <span class="pl-k">-e</span> <span class="pl-s"><span class="pl-pds">'</span>libhts.a<span class="pl-pds">'</span></span> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>Compile didn't complete. No libhts.a library file found<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC927" class="react-file-line html-div" data-testid="code-cell" data-line-number="927" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC928" class="react-file-line html-div" data-testid="code-cell" data-line-number="928" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$curdir</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC929" class="react-file-line html-div" data-testid="code-cell" data-line-number="929" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$retval</span> = Cwd::realpath(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$htslib_install_dir</span>/htslib<span class="pl-pds">"</span></span>) ;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC930" class="react-file-line html-div" data-testid="code-cell" data-line-number="930" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC931" class="react-file-line html-div" data-testid="code-cell" data-line-number="931" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC932" class="react-file-line html-div" data-testid="code-cell" data-line-number="932" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC933" class="react-file-line html-div" data-testid="code-cell" data-line-number="933" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> INSTALL Bio::DB::HTS</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC934" class="react-file-line html-div" data-testid="code-cell" data-line-number="934" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#####################</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC935" class="react-file-line html-div" data-testid="code-cell" data-line-number="935" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">install_biodbhts</span>() {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC936" class="react-file-line html-div" data-testid="code-cell" data-line-number="936" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC937" class="react-file-line html-div" data-testid="code-cell" data-line-number="937" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span>Attempting to install Bio::DB::HTS and htslib.<span class="pl-cce">\n\n</span>>>> If this fails, try re-running with --NO_HTSLIB<span class="pl-cce">\n\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC938" class="react-file-line html-div" data-testid="code-cell" data-line-number="938" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC939" class="react-file-line html-div" data-testid="code-cell" data-line-number="939" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$htslib_location</span> = install_htslib();</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC940" class="react-file-line html-div" data-testid="code-cell" data-line-number="940" style="position:relative"> rmtree( <span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/tmp<span class="pl-pds">'</span></span> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC941" class="react-file-line html-div" data-testid="code-cell" data-line-number="941" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC942" class="react-file-line html-div" data-testid="code-cell" data-line-number="942" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span>Now install Bio::DB::HTS proper</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC943" class="react-file-line html-div" data-testid="code-cell" data-line-number="943" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$biodbhts_github_url</span> = <span class="pl-s"><span class="pl-pds">"</span>https://github.com/Ensembl/Bio-DB-HTS<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC944" class="react-file-line html-div" data-testid="code-cell" data-line-number="944" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$biodbhts_zip_github_url</span> = <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$biodbhts_github_url</span>/archive/<span class="pl-smi">$BIOHTS_VERSION</span>.zip<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC945" class="react-file-line html-div" data-testid="code-cell" data-line-number="945" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$biodbhts_zip_download_file</span> = <span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/tmp/biodbhts.zip<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC946" class="react-file-line html-div" data-testid="code-cell" data-line-number="946" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC947" class="react-file-line html-div" data-testid="code-cell" data-line-number="947" style="position:relative"> <span class="pl-c1">mkdir</span> <span class="pl-smi">$DEST_DIR</span> <span class="pl-k">unless</span> <span class="pl-k">-d</span> <span class="pl-smi">$DEST_DIR</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC948" class="react-file-line html-div" data-testid="code-cell" data-line-number="948" style="position:relative"> <span class="pl-c1">mkdir</span> <span class="pl-smi">$DEST_DIR</span>.<span class="pl-s"><span class="pl-pds">'</span>/tmp<span class="pl-pds">'</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC949" class="react-file-line html-div" data-testid="code-cell" data-line-number="949" style="position:relative"> download_to_file(<span class="pl-smi">$biodbhts_zip_github_url</span>, <span class="pl-smi">$biodbhts_zip_download_file</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC950" class="react-file-line html-div" data-testid="code-cell" data-line-number="950" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span> - unpacking <span class="pl-smi">$biodbhts_zip_download_file</span> to <span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC951" class="react-file-line html-div" data-testid="code-cell" data-line-number="951" style="position:relative"> unpack_arch(<span class="pl-smi">$biodbhts_zip_download_file</span>, <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-pds">"</span></span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC952" class="react-file-line html-div" data-testid="code-cell" data-line-number="952" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC953" class="react-file-line html-div" data-testid="code-cell" data-line-number="953" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$tmp_name</span> = <span class="pl-k">-d</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/Bio-HTS-<span class="pl-smi">$BIOHTS_VERSION</span><span class="pl-pds">"</span></span> ? <span class="pl-s"><span class="pl-pds">"</span>Bio-HTS-<span class="pl-smi">$BIOHTS_VERSION</span><span class="pl-pds">"</span></span> : <span class="pl-s"><span class="pl-pds">"</span>Bio-DB-HTS-<span class="pl-smi">$BIOHTS_VERSION</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC954" class="react-file-line html-div" data-testid="code-cell" data-line-number="954" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC955" class="react-file-line html-div" data-testid="code-cell" data-line-number="955" style="position:relative"> <span class="pl-c1">print</span> <span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-smi">$tmp_name</span> - moving files to <span class="pl-smi">$BIODBHTS_DIR</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span> <span class="pl-k">unless</span> <span class="pl-smi">$QUIET</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC956" class="react-file-line html-div" data-testid="code-cell" data-line-number="956" style="position:relative"> rmtree(<span class="pl-smi">$BIODBHTS_DIR</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC957" class="react-file-line html-div" data-testid="code-cell" data-line-number="957" style="position:relative"> move(<span class="pl-s"><span class="pl-pds">"</span><span class="pl-smi">$DEST_DIR</span>/tmp/<span class="pl-smi">$tmp_name</span><span class="pl-pds">"</span></span>, <span class="pl-smi">$BIODBHTS_DIR</span>) <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not move directory<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>.<span class="pl-smi">$!</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC958" class="react-file-line html-div" data-testid="code-cell" data-line-number="958" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC959" class="react-file-line html-div" data-testid="code-cell" data-line-number="959" style="position:relative"> <span class="pl-c1">print</span>( <span class="pl-s"><span class="pl-pds">"</span> - making Bio::DB:HTS<span class="pl-cce">\n</span><span class="pl-pds">"</span></span> );</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC960" class="react-file-line html-div" data-testid="code-cell" data-line-number="960" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span> patch makefile</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC961" class="react-file-line html-div" data-testid="code-cell" data-line-number="961" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$BIODBHTS_DIR</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC962" class="react-file-line html-div" data-testid="code-cell" data-line-number="962" style="position:relative"> <span class="pl-c1">system</span> <span class="pl-s"><span class="pl-pds">"</span>perl Build.PL --htslib <span class="pl-smi">$htslib_location</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC963" class="react-file-line html-div" data-testid="code-cell" data-line-number="963" style="position:relative"> <span class="pl-c1">system</span> <span class="pl-s"><span class="pl-pds">"</span>./Build<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC964" class="react-file-line html-div" data-testid="code-cell" data-line-number="964" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-s"><span class="pl-pds">"</span>.<span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC965" class="react-file-line html-div" data-testid="code-cell" data-line-number="965" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC966" class="react-file-line html-div" data-testid="code-cell" data-line-number="966" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span>move the library</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC967" class="react-file-line html-div" data-testid="code-cell" data-line-number="967" style="position:relative"> <span class="pl-k">my</span> <span class="pl-smi">$pdir</span> = getcwd;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC968" class="react-file-line html-div" data-testid="code-cell" data-line-number="968" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC969" class="react-file-line html-div" data-testid="code-cell" data-line-number="969" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span>Perl modules to go alongside the API</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC970" class="react-file-line html-div" data-testid="code-cell" data-line-number="970" style="position:relative"> dircopy(<span class="pl-s"><span class="pl-pds">"</span>lib/Bio<span class="pl-pds">"</span></span>,<span class="pl-smi">$REALPATH_DEST_DIR</span>);</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC971" class="react-file-line html-div" data-testid="code-cell" data-line-number="971" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC972" class="react-file-line html-div" data-testid="code-cell" data-line-number="972" style="position:relative"> <span class="pl-c"><span class="pl-c">#</span>The shared object XS library</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC973" class="react-file-line html-div" data-testid="code-cell" data-line-number="973" style="position:relative"> <span class="pl-k">if</span>( <span class="pl-k">-e</span> <span class="pl-s"><span class="pl-pds">"</span>blib/arch/auto/Bio/DB/HTS/HTS.so<span class="pl-pds">"</span></span> ) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC974" class="react-file-line html-div" data-testid="code-cell" data-line-number="974" style="position:relative"> copy( <span class="pl-s"><span class="pl-pds">"</span>blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>..<span class="pl-pds">"</span></span>)</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC975" class="react-file-line html-div" data-testid="code-cell" data-line-number="975" style="position:relative"> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not copy shared Faidx.so library:<span class="pl-smi">$!</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC976" class="react-file-line html-div" data-testid="code-cell" data-line-number="976" style="position:relative"> copy( <span class="pl-s"><span class="pl-pds">"</span>blib/arch/auto/Bio/DB/HTS/HTS.so<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>..<span class="pl-pds">"</span></span>)</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC977" class="react-file-line html-div" data-testid="code-cell" data-line-number="977" style="position:relative"> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not copy shared HTS.so library:<span class="pl-smi">$!</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC978" class="react-file-line html-div" data-testid="code-cell" data-line-number="978" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC979" class="react-file-line html-div" data-testid="code-cell" data-line-number="979" style="position:relative"> <span class="pl-k">elsif</span>( <span class="pl-k">-e</span> <span class="pl-s"><span class="pl-pds">"</span>blib/arch/auto/Bio/DB/HTS/HTS.bundle<span class="pl-pds">"</span></span> ) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC980" class="react-file-line html-div" data-testid="code-cell" data-line-number="980" style="position:relative"> copy( <span class="pl-s"><span class="pl-pds">"</span>blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bundle<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>..<span class="pl-pds">"</span></span>)</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC981" class="react-file-line html-div" data-testid="code-cell" data-line-number="981" style="position:relative"> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not copy shared Faidx.bundle library:<span class="pl-smi">$!</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC982" class="react-file-line html-div" data-testid="code-cell" data-line-number="982" style="position:relative"> copy( <span class="pl-s"><span class="pl-pds">"</span>blib/arch/auto/Bio/DB/HTS/HTS.bundle<span class="pl-pds">"</span></span>, <span class="pl-s"><span class="pl-pds">"</span>..<span class="pl-pds">"</span></span>)</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC983" class="react-file-line html-div" data-testid="code-cell" data-line-number="983" style="position:relative"> <span class="pl-k">or</span> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Could not copy shared HTS.bundle library:<span class="pl-smi">$!</span><span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC984" class="react-file-line html-div" data-testid="code-cell" data-line-number="984" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC985" class="react-file-line html-div" data-testid="code-cell" data-line-number="985" style="position:relative"> <span class="pl-k">else</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC986" class="react-file-line html-div" data-testid="code-cell" data-line-number="986" style="position:relative"> <span class="pl-k">die</span> <span class="pl-s"><span class="pl-pds">"</span>ERROR: Shared Bio::DB:HTS library not found<span class="pl-cce">\n</span><span class="pl-pds">"</span></span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC987" class="react-file-line html-div" data-testid="code-cell" data-line-number="987" style="position:relative"> }</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC988" class="react-file-line html-div" data-testid="code-cell" data-line-number="988" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC989" class="react-file-line html-div" data-testid="code-cell" data-line-number="989" style="position:relative"> <span class="pl-c1">chdir</span> <span class="pl-smi">$pdir</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC990" class="react-file-line html-div" data-testid="code-cell" data-line-number="990" style="position:relative">}</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC991" class="react-file-line html-div" data-testid="code-cell" data-line-number="991" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC992" class="react-file-line html-div" data-testid="code-cell" data-line-number="992" style="position:relative"><span class="pl-k">sub</span> <span class="pl-en">dircopy</span> {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC993" class="react-file-line html-div" data-testid="code-cell" data-line-number="993" style="position:relative"> <span class="pl-k">my</span> (<span class="pl-smi">$from</span>, <span class="pl-smi">$to</span>) = <span class="pl-smi">@_</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC994" class="react-file-line html-div" data-testid="code-cell" data-line-number="994" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC995" class="react-file-line html-div" data-testid="code-cell" data-line-number="995" style="position:relative"> <span class="pl-c1">opendir</span> FROM, <span class="pl-smi">$from</span>;</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC996" class="react-file-line html-div" data-testid="code-cell" data-line-number="996" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC997" class="react-file-line html-div" data-testid="code-cell" data-line-number="997" style="position:relative"> <span class="pl-k">foreach</span> <span class="pl-k">my</span> <span class="pl-smi">$file</span>(<span class="pl-c1">grep</span> {!/^\.\.?/} <span class="pl-c1">readdir</span> FROM) {</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC998" class="react-file-line html-div" data-testid="code-cell" data-line-number="998" style="position:relative"> </div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC999" class="react-file-line html-div" data-testid="code-cell" 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0 0 0 .22.368h12.164a.25.25 0 0 0 .22-.368Zm.53 3.996v2.5a.75.75 0 0 1-1.5 0v-2.5a.75.75 0 0 1 1.5 0ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"></path> </svg> <button type="button" class="flash-close js-ajax-error-dismiss" aria-label="Dismiss error"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg> </button> You can’t perform that action at this time. </div> <template id="site-details-dialog"> <details class="details-reset details-overlay details-overlay-dark lh-default color-fg-default hx_rsm" open> <summary role="button" aria-label="Close dialog"></summary> <details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast hx_rsm-dialog hx_rsm-modal"> <button class="Box-btn-octicon m-0 btn-octicon position-absolute right-0 top-0" type="button" aria-label="Close dialog" data-close-dialog> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x"> <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path> </svg> </button> <div class="octocat-spinner my-6 js-details-dialog-spinner"></div> </details-dialog> </details> </template> <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;"> <div class="Popover-message Popover-message--bottom-left Popover-message--large Box color-shadow-large" style="width:360px;"> </div> </div> <template id="snippet-clipboard-copy-button"> <div class="zeroclipboard-container position-absolute right-0 top-0"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn js-clipboard-copy m-2 p-0" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon m-2"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none m-2"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> <template id="snippet-clipboard-copy-button-unpositioned"> <div class="zeroclipboard-container"> <clipboard-copy aria-label="Copy" class="ClipboardButton btn btn-invisible js-clipboard-copy m-2 p-0 d-flex flex-justify-center flex-items-center" data-copy-feedback="Copied!" data-tooltip-direction="w"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon"> <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path> </svg> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none"> <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path> </svg> </clipboard-copy> </div> </template> </div> <div id="js-global-screen-reader-notice" class="sr-only mt-n1" aria-live="polite" aria-atomic="true" ></div> <div id="js-global-screen-reader-notice-assertive" class="sr-only mt-n1" aria-live="assertive" aria-atomic="true"></div> </body> </html>