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Interface</a></li> <li class="toctree-l3"><a class="reference internal" href="cli_services.html">Using BV-BRC Services from the Command Line</a></li> <li class="toctree-l3"><a class="reference internal" href="cli_common_tasks.html">Common Tasks With P3 Scripts</a></li> <li class="toctree-l3"><a class="reference internal" href="cli_clustering.html">Looking for Hypothetical Proteins in Clusters of Related Features</a></li> <li class="toctree-l3"><a class="reference internal" href="cli_signature_clusters.html">Computing Signature Clusters: an Application of the Command-Line Tools</a></li> <li class="toctree-l3"><a class="reference internal" href="command_list/index.html">BV-BRC Command Line Program Reference</a></li> </ul> </li> <li class="toctree-l2"><a class="reference internal" href="#rast-tutorials">RAST Tutorials</a><ul> <li class="toctree-l3"><a class="reference internal" href="rasttk_getting_started.html">RASTtk: Getting Started With The Default Pipeline</a></li> <li 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menu" style="background: #e3e3e3" > <i data-toggle="wy-nav-top" class="fa fa-bars"></i> <a href="../index.html">BV-BRC</a> </nav> <div class="wy-nav-content"> <div class="rst-content"> <div role="navigation" aria-label="Page navigation"> <ul class="wy-breadcrumbs"> <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li> <li class="breadcrumb-item active">Command Line Interface</li> <li class="wy-breadcrumbs-aside"> <a href="../_sources/cli_tutorial/index.rst.txt" rel="nofollow"> View page source</a> </li> </ul> <hr/> </div> <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article"> <div itemprop="articleBody"> <section id="command-line-interface"> <h1>Command Line Interface<a class="headerlink" href="#command-line-interface" title="Permalink to this heading">露</a></h1> <p><a class="reference external" href="https://www.bv-brc.org">BV-BRC</a> is an integration of different types of data and software tools that support research on bacterial and viral pathogens. The typical biologist seeking access to the BV-BRC data and tools will usually explore the web-based user interface. However, there are many instances in which programatic or command-line interfaces are more suitable. For users that wish command-line access to BV-BRC, we provide the tools described in this document. We call these tools the <em>P3-scripts</em>. They are intended to run on your machine, going over the network to access the services provided by BV-BRC.</p> <section id="installing-the-cli-release"> <h2>Installing the CLI Release<a class="headerlink" href="#installing-the-cli-release" title="Permalink to this heading">露</a></h2> <p>Since the CLI tools run on your computer, to use them you will need to download and install a software package in order to use them.</p> <p>We currently have Windows, macOS and Debian/Ubuntu releases of the BV-BRC Command Line Interface.</p> <p>The releases are available at the <a class="reference external" href="https://github.com/BV-BRC/BV-BRC-CLI/releases">BV-BRC github site</a>. Full installation instructions are available in <a class="reference internal" href="cli_installation.html#cli-installation"><span class="std std-ref">Installing the BV-BRC Command Line Interface</span></a>.</p> </section> <section id="tutorials-and-reference-documentation"> <h2>Tutorials and Reference Documentation<a class="headerlink" href="#tutorials-and-reference-documentation" title="Permalink to this heading">露</a></h2> <p>In order to enable users to make the most of the BV-BRC command line interface we have collected a number of tutorials and reference materials. This collection is linked below.</p> <div class="toctree-wrapper compound"> <p class="caption" role="heading"><span class="caption-text">Tutorials:</span></p> <ul> <li class="toctree-l1"><a class="reference internal" href="cli_installation.html">Installing the BV-BRC Command Line Interface</a></li> <li class="toctree-l1"><a class="reference internal" href="cli_getting_started.html">Using the BV-BRC Command-line Interface</a></li> <li class="toctree-l1"><a class="reference internal" href="cli_services.html">Using BV-BRC Services from the Command Line</a></li> <li class="toctree-l1"><a class="reference internal" href="cli_common_tasks.html">Common Tasks With P3 Scripts</a></li> <li class="toctree-l1"><a class="reference internal" href="cli_clustering.html">Looking for Hypothetical Proteins in Clusters of Related Features</a></li> <li class="toctree-l1"><a class="reference internal" href="cli_signature_clusters.html">Computing Signature Clusters: an Application of the Command-Line Tools</a></li> </ul> </div> <div class="toctree-wrapper compound"> <p class="caption" role="heading"><span class="caption-text">Reference documentation:</span></p> <ul> <li class="toctree-l1"><a class="reference internal" href="command_list/index.html">BV-BRC Command Line Program Reference</a></li> </ul> </div> </section> <section id="rast-tutorials"> <h2>RAST Tutorials<a class="headerlink" href="#rast-tutorials" title="Permalink to this heading">露</a></h2> <p>We are also making available here a set of tutorials that relate to the RAST and RASTtk projects. The RAST technology underlies the genome annotation services provided by BV-BRC.</p> <div class="toctree-wrapper compound"> <p class="caption" role="heading"><span class="caption-text">RAST tutorials:</span></p> <ul> <li class="toctree-l1"><a class="reference internal" href="rasttk_getting_started.html">RASTtk: Getting Started With The Default Pipeline</a></li> <li class="toctree-l1"><a class="reference internal" href="rasttk_incremental_commands.html">RASTtk, The Incremental Commands</a></li> </ul> </div> </section> </section> </div> </div> <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer"> <a href="../tutorial/compare_region_viewer/compare_region_viewer.html" class="btn btn-neutral float-left" title="Compare Region Viewer" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a> <a href="cli_installation.html" class="btn btn-neutral float-right" title="Installing the BV-BRC Command Line Interface" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a> </div> <hr/> <div role="contentinfo"> <p>© Copyright 2023 | The BV-BRC Team.</p> </div> Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. </footer> </div> </div> </section> </div> <script> jQuery(function () { SphinxRtdTheme.Navigation.enable(true); }); </script> <script> var logo = '<img src="https://www.bv-brc.org/docs/_static/bvbrc-logo-blue.png" class="logo" alt="BV-BRC Logo">'; var home = '<div class="branding"><a href="https://bv-brc.org" title="BV-BRC Homepage">BV-BRC Home</a> &rsaquo; <a href="/docs/" title="BV-BRC Documentation">Docs</a></div>'; $(".wy-side-nav-search").prepend(home).prepend(logo); </script>  <script async src="https://www.googletagmanager.com/gtag/js?id=G-GS8F60MG56"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-GS8F60MG56'); </script>  <script async src="https://www.googletagmanager.com/gtag/js?id=UA-165638318-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-165638318-1'); </script> </body> </html>