forked from msioda/BioLockJ
-
Notifications
You must be signed in to change notification settings - Fork 12
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
426 changed files
with
2,573 additions
and
1,222 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| v1.2.6-dev | ||
| v1.2.7 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,224 @@ | ||
| <!DOCTYPE html> | ||
| <!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]--> | ||
| <!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]--> | ||
| <head> | ||
| <meta charset="utf-8"> | ||
| <meta http-equiv="X-UA-Compatible" content="IE=edge"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1.0"> | ||
|
|
||
| <meta name="author" content="Ivory Blakley"> | ||
| <link rel="shortcut icon" href="../img/favicon.ico"> | ||
| <title>Check Dependencies - BioLockJ User Guide</title> | ||
| <link href='https://fonts.googleapis.com/css?family=Lato:400,700|Roboto+Slab:400,700|Inconsolata:400,700' rel='stylesheet' type='text/css'> | ||
|
|
||
| <link rel="stylesheet" href="../css/theme.css" type="text/css" /> | ||
| <link rel="stylesheet" href="../css/theme_extra.css" type="text/css" /> | ||
| <link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/github.min.css"> | ||
|
|
||
| <script> | ||
| // Current page data | ||
| var mkdocs_page_name = "Check Dependencies"; | ||
| var mkdocs_page_input_path = "Check-Dependencies.md"; | ||
| var mkdocs_page_url = null; | ||
| </script> | ||
|
|
||
| <script src="../js/jquery-2.1.1.min.js" defer></script> | ||
| <script src="../js/modernizr-2.8.3.min.js" defer></script> | ||
| <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script> | ||
| <script>hljs.initHighlightingOnLoad();</script> | ||
|
|
||
| </head> | ||
|
|
||
| <body class="wy-body-for-nav" role="document"> | ||
|
|
||
| <div class="wy-grid-for-nav"> | ||
|
|
||
|
|
||
| <nav data-toggle="wy-nav-shift" class="wy-nav-side stickynav"> | ||
| <div class="wy-side-nav-search"> | ||
| <a href=".." class="icon icon-home"> BioLockJ User Guide</a> | ||
| <div role="search"> | ||
| <form id ="rtd-search-form" class="wy-form" action="../search.html" method="get"> | ||
| <input type="text" name="q" placeholder="Search docs" title="Type search term here" /> | ||
| </form> | ||
| </div> | ||
| </div> | ||
|
|
||
| <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation"> | ||
| <ul class="current"> | ||
|
|
||
|
|
||
| <li class="toctree-l1"> | ||
|
|
||
| <a class="" href="..">Home</a> | ||
| </li> | ||
|
|
||
| <li class="toctree-l1"> | ||
|
|
||
| <a class="" href="../Getting-Started/">Getting Started</a> | ||
| </li> | ||
|
|
||
| <li class="toctree-l1"> | ||
|
|
||
| <a class="" href="../Commands/">Commands</a> | ||
| </li> | ||
|
|
||
| <li class="toctree-l1"> | ||
|
|
||
| <span class="caption-text">Pipeline Componenets</span> | ||
| <ul class="subnav"> | ||
| <li class=""> | ||
|
|
||
| <a class="" href="../Configuration/">Configuration</a> | ||
| </li> | ||
| <li class=""> | ||
|
|
||
| <a class="" href="../Built-in-modules/">Modules</a> | ||
| </li> | ||
| <li class=""> | ||
|
|
||
| <a class="" href="../The-Metadata-File/">Metadata</a> | ||
| </li> | ||
| <li class=""> | ||
|
|
||
| <a class="" href="../Dependencies/">Dependencies</a> | ||
| </li> | ||
| </ul> | ||
| </li> | ||
|
|
||
| <li class="toctree-l1"> | ||
|
|
||
| <span class="caption-text">Features</span> | ||
| <ul class="subnav"> | ||
| <li class=" current"> | ||
|
|
||
| <a class="current" href="./">Check Dependencies</a> | ||
| <ul class="subnav"> | ||
|
|
||
| <li class="toctree-l3"><a href="#precheck-a-pipeline">Precheck a pipeline</a></li> | ||
|
|
||
|
|
||
| </ul> | ||
| </li> | ||
| <li class=""> | ||
|
|
||
| <a class="" href="../Failure-Recovery/">Failure Recovery</a> | ||
| </li> | ||
| <li class=""> | ||
|
|
||
| <a class="" href="../Validation/">Validation</a> | ||
| </li> | ||
| <li class=""> | ||
|
|
||
| <a class="" href="../Building-Modules/">Building Modules</a> | ||
| </li> | ||
| </ul> | ||
| </li> | ||
|
|
||
| <li class="toctree-l1"> | ||
|
|
||
| <a class="" href="../Example-Pipeline/">Example Pipeline</a> | ||
| </li> | ||
|
|
||
| <li class="toctree-l1"> | ||
|
|
||
| <a class="" href="../FAQ/">FAQ</a> | ||
| </li> | ||
|
|
||
| </ul> | ||
| </div> | ||
| | ||
| </nav> | ||
|
|
||
| <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"> | ||
|
|
||
|
|
||
| <nav class="wy-nav-top" role="navigation" aria-label="top navigation"> | ||
| <i data-toggle="wy-nav-top" class="fa fa-bars"></i> | ||
| <a href="..">BioLockJ User Guide</a> | ||
| </nav> | ||
|
|
||
|
|
||
| <div class="wy-nav-content"> | ||
| <div class="rst-content"> | ||
| <div role="navigation" aria-label="breadcrumbs navigation"> | ||
| <ul class="wy-breadcrumbs"> | ||
| <li><a href="..">Docs</a> »</li> | ||
|
|
||
|
|
||
|
|
||
| <li>Features »</li> | ||
|
|
||
|
|
||
|
|
||
| <li>Check Dependencies</li> | ||
| <li class="wy-breadcrumbs-aside"> | ||
|
|
||
| </li> | ||
| </ul> | ||
| <hr/> | ||
| </div> | ||
| <div role="main"> | ||
| <div class="section"> | ||
|
|
||
| <p>BioLockJ is designed find all problems in one sitting. Every module includes a <em>check dependencies</em> method, which quickly detects issues that would cause an error during execution. This is run for all modules in a pipeline <em>before</em> the first module executes. </p> | ||
| <p>When BioLockJ runs, it has three major phases: </p> | ||
| <ul> | ||
| <li>pipeline formation - string together the modues specified in the config file along with any additional modules that the program adds on the users behalf; and initiate the utilities needed for the pipeline (such as docker, metadata, determine input type).</li> | ||
| <li>check dependencies - scan the pipeline for anything that may cause an error during execution</li> | ||
| <li>run pipeline - execute each module in the sequence.</li> | ||
| </ul> | ||
| <h2 id="precheck-a-pipeline">Precheck a pipeline</h2> | ||
| <p>By including the <code>--precheck-only</code> argument (or <code>-p</code>) when running <code>biolockj</code>; you are running in <strong>precheck</strong> mode. BioLockJ will do the first two phases, and then stop. This allows you to quickly test changes to your pipeline configuration without actually running a pipeline. It also allows you to see any modules that are automatically added to your pipeline.</p> | ||
|
|
||
| </div> | ||
| </div> | ||
| <footer> | ||
|
|
||
| <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation"> | ||
|
|
||
| <a href="../Failure-Recovery/" class="btn btn-neutral float-right" title="Failure Recovery">Next <span class="icon icon-circle-arrow-right"></span></a> | ||
|
|
||
|
|
||
| <a href="../Dependencies/" class="btn btn-neutral" title="Dependencies"><span class="icon icon-circle-arrow-left"></span> Previous</a> | ||
|
|
||
| </div> | ||
|
|
||
|
|
||
| <hr/> | ||
|
|
||
| <div role="contentinfo"> | ||
| <!-- Copyright etc --> | ||
|
|
||
| <p>2019 Fodor Lab</p> | ||
|
|
||
| </div> | ||
|
|
||
| Built with <a href="http://www.mkdocs.org">MkDocs</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. | ||
| </footer> | ||
|
|
||
| </div> | ||
| </div> | ||
|
|
||
| </section> | ||
|
|
||
| </div> | ||
|
|
||
| <div class="rst-versions" role="note" style="cursor: pointer"> | ||
| <span class="rst-current-version" data-toggle="rst-current-version"> | ||
|
|
||
|
|
||
| <span><a href="../Dependencies/" style="color: #fcfcfc;">« Previous</a></span> | ||
|
|
||
|
|
||
| <span style="margin-left: 15px"><a href="../Failure-Recovery/" style="color: #fcfcfc">Next »</a></span> | ||
|
|
||
| </span> | ||
| </div> | ||
| <script>var base_url = '..';</script> | ||
| <script src="../js/theme.js" defer></script> | ||
| <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML" defer></script> | ||
| <script src="../search/main.js" defer></script> | ||
|
|
||
| </body> | ||
| </html> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.