Merge pull request #43 from necrolyte2/master

pip caching, uninstall and html docs
VDBWRAIR · Dec 5, 2014 · d1e7fdd · d1e7fdd
2 parents 5ec5778 + 42003a0
commit d1e7fdd
Show file tree

Hide file tree

Showing 92 changed files with 10,701 additions and 5 deletions.
diff --git a/.gitignore b/.gitignore
@@ -73,5 +73,6 @@ usamriidPathDiscov/download/bwa-*
 usamriidPathDiscov/download/htslib-*
 usamriidPathDiscov/download/samtools-*
 usamriidPathDiscov/download/fastqc*
+usamriidPathDiscov/download/.pip_cache
 
 #Negate, include the file
diff --git a/docs/build/doctrees/configuration.doctree b/docs/build/doctrees/configuration.doctree
diff --git a/docs/build/doctrees/databases.doctree b/docs/build/doctrees/databases.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/index.doctree b/docs/build/doctrees/index.doctree
diff --git a/docs/build/doctrees/install.doctree b/docs/build/doctrees/install.doctree
diff --git a/docs/build/doctrees/make_pie.doctree b/docs/build/doctrees/make_pie.doctree
diff --git a/docs/build/doctrees/make_summary.doctree b/docs/build/doctrees/make_summary.doctree
diff --git a/docs/build/doctrees/modules.doctree b/docs/build/doctrees/modules.doctree
diff --git a/docs/build/doctrees/stages/host_map.doctree b/docs/build/doctrees/stages/host_map.doctree
diff --git a/docs/build/doctrees/stages/index.doctree b/docs/build/doctrees/stages/index.doctree
diff --git a/docs/build/doctrees/stages/iterative_blast_phylo.doctree b/docs/build/doctrees/stages/iterative_blast_phylo.doctree
diff --git a/docs/build/doctrees/stages/orf_filter.doctree b/docs/build/doctrees/stages/orf_filter.doctree
diff --git a/docs/build/doctrees/stages/quality_filter.doctree b/docs/build/doctrees/stages/quality_filter.doctree
diff --git a/docs/build/doctrees/stages/ray2_assembly.doctree b/docs/build/doctrees/stages/ray2_assembly.doctree
diff --git a/docs/build/doctrees/stages/ray_assembly.doctree b/docs/build/doctrees/stages/ray_assembly.doctree
diff --git a/docs/build/doctrees/stages/step1.doctree b/docs/build/doctrees/stages/step1.doctree
diff --git a/docs/build/doctrees/usamriidPathDiscov.doctree b/docs/build/doctrees/usamriidPathDiscov.doctree
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: a12f42fec580dd5633381321fbc712b6
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_images/example_make_pie.png b/docs/build/html/_images/example_make_pie.png
diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -0,0 +1,198 @@
+
+
+<!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 name="viewport" content="width=device-width, initial-scale=1.0">
+
+  <title>Overview: module code &mdash; USAMRIID Pathogen Descovery 4.0 documentation</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="../_static/css/theme.css" type="text/css" />
+
+
+
+    <link rel="top" title="USAMRIID Pathogen Descovery 4.0 documentation" href="../index.html"/> 
+
+
+  <script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></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">
+      <div class="wy-side-nav-search">
+        <a href="../index.html" class="fa fa-home"> USAMRIID Pathogen Descovery</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" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+      </div>
+
+      <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+            <ul>
+<li class="toctree-l1"><a class="reference internal" href="../install.html">Installation</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../install.html#system-packages">System Packages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../install.html#id1">Installation</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../databases.html">Databases</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../databases.html#directory-setup">Directory Setup</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../databases.html#blast">Blast</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../databases.html#host-genome">Host Genome</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../configuration.html">Configuration</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../configuration.html#config-yaml-base">usamriidPathDiscov/files/config.yaml.base</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../configuration.html#sample-param-base">usamriidPathDiscov/files/sample.param.base</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../stages/index.html">Pipeline Stages</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../stages/step1.html">step1</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../stages/host_map.html">host_map</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../stages/quality_filter.html">quality_filter</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../stages/ray2_assembly.html">ray_assembly</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../stages/orf_filter.html">orf_filter</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../stages/iterative_blast_phylo.html">iterative_blast_phylo</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../make_summary.html">make_summary</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../make_summary.html#reading-the-report">Reading the Report</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../make_pie.html">make_pie</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../make_pie.html#example">Example</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../make_pie.html#vector-composition">Vector Composition</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../make_pie.html#host-composition">Host Composition</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../make_pie.html#pathogen-composition">Pathogen Composition</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../make_pie.html#sample-composition">Sample Composition</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">usamriidPathDiscov</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../usamriidPathDiscov.html">usamriidPathDiscov package</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="../uninstall.html">Uninstall</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="../uninstall.html#partial-uninstall">Partial Uninstall</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../uninstall.html#full-uninstall">Full Uninstall</a></li>
+</ul>
+</li>
+</ul>
+
+
+      </div>
+      &nbsp;
+    </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="../index.html">USAMRIID Pathogen Descovery</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="../index.html">Docs</a> &raquo;</li>
+
+    <li>Overview: module code</li>
+      <li class="wy-breadcrumbs-aside">
+
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main">
+
+  <h1>All modules for which code is available</h1>
+<ul><li><a href="usamriidPathDiscov/make_pie.html">usamriidPathDiscov.make_pie</a></li>
+<li><a href="usamriidPathDiscov/make_summary.html">usamriidPathDiscov.make_summary</a></li>
+<li><a href="usamriidPathDiscov/verifyproject.html">usamriidPathDiscov.verifyproject</a></li>
+</ul>
+
+          </div>
+          <footer>
+
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2014 Mike Wiley, Gustavo Palacios, Jason Ladner, Dereje Jima.
+    </p>
+  </div>
+
+  <a href="https://github.com/snide/sphinx_rtd_theme">Sphinx theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>
+</footer>
+        </div>
+      </div>
+
+    </section>
+
+  </div>
+
+
+
+
+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'../',
+            VERSION:'4.0',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true
+        };
+    </script>
+      <script type="text/javascript" src="../_static/jquery.js"></script>
+      <script type="text/javascript" src="../_static/underscore.js"></script>
+      <script type="text/javascript" src="../_static/doctools.js"></script>
+
+
+
+
+
+    <script type="text/javascript" src="../_static/js/theme.js"></script>
+
+
+
+
+  <script type="text/javascript">
+      jQuery(function () {
+          SphinxRtdTheme.StickyNav.enable();
+      });
+  </script>
+
+
+</body>
+</html>