documentation update

CGAT-Group · Jan 3, 2022 · bfb603e · bfb603e
1 parent df930cf
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Showing 59 changed files with 486 additions and 139 deletions.
diff --git a/docs/build/doctrees/contents.doctree b/docs/build/doctrees/contents.doctree
diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/further-information/faq.doctree b/docs/build/doctrees/further-information/faq.doctree
diff --git a/docs/build/doctrees/further-information/uninstall-dicast.doctree b/docs/build/doctrees/further-information/uninstall-dicast.doctree
diff --git a/docs/build/html/_sources/contents.rst.txt b/docs/build/html/_sources/contents.rst.txt
@@ -66,4 +66,5 @@ DICAST is currently hosted on `bioRxiv`_, at this link <notsubmitted-yet>.
 
 	further-information/example-files
 	further-information/faq
+	further-information/uninstall-dicast	
 	further-information/about
diff --git a/docs/build/html/_sources/further-information/faq.rst.txt b/docs/build/html/_sources/further-information/faq.rst.txt
@@ -10,3 +10,4 @@ Q: How do I contribute to DICAST?
 
 .. toctree::
    :maxdepth: 2
+    further-information/uninstall-dicast
diff --git a/docs/build/html/_sources/further-information/uninstall-dicast.rst.txt b/docs/build/html/_sources/further-information/uninstall-dicast.rst.txt
@@ -0,0 +1,7 @@
+Uninstalling DICAST
+===================
+
+In order to uninstall dicast, please execute the script with: 
+  ``bash scripts/uninstall-dicast.sh``
+
+We hope DICAST served you well, please remember to cite DICAST, should you have found it useful.
diff --git a/docs/build/html/_sources/get-started/setup.rst.txt b/docs/build/html/_sources/get-started/setup.rst.txt
@@ -11,3 +11,4 @@ Please follow these steps carefully to set up your working environment.
    setup/input
    setup/docker
    setup/snakemake
+
diff --git a/docs/build/html/contents.html b/docs/build/html/contents.html
@@ -158,9 +158,8 @@
 <li class="toctree-l1"><a class="reference internal" href="further-information/example-files.html">Examples</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="further-information/faq.html">FAQ</a><ul class="simple">
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="further-information/faq.html">FAQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="further-information/uninstall-dicast.html">Uninstalling DICAST</a></li>
 <li class="toctree-l1"><a class="reference internal" href="further-information/about.html">About</a><ul class="simple">
 </ul>
 </li>

diff --git a/docs/build/html/further-information/about.html b/docs/build/html/further-information/about.html
@@ -39,7 +39,7 @@
   <link rel="stylesheet" href="../_static/_templates/custom.css" type="text/css" />
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="prev" title="FAQ" href="faq.html" /> 
+    <link rel="prev" title="Uninstalling DICAST" href="uninstall-dicast.html" /> 
 </head>
 
 <body class="wy-body-for-nav">
@@ -158,9 +158,8 @@
 <li class="toctree-l1"><a class="reference internal" href="example-files.html">Examples</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="faq.html">FAQ</a><ul class="simple">
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="faq.html">FAQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="uninstall-dicast.html">Uninstalling DICAST</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">About</a><ul class="simple">
 </ul>
 </li>
@@ -268,7 +267,7 @@ <h2>Contact us<a class="headerlink" href="#contact-us" title="Permalink to this
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
 
-        <a href="faq.html" class="btn btn-neutral float-left" title="FAQ" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="uninstall-dicast.html" class="btn btn-neutral float-left" title="Uninstalling DICAST" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 

diff --git a/docs/build/html/further-information/example-files.html b/docs/build/html/further-information/example-files.html
@@ -159,9 +159,8 @@
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Examples</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="faq.html">FAQ</a><ul class="simple">
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="faq.html">FAQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="uninstall-dicast.html">Uninstalling DICAST</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About</a><ul class="simple">
 </ul>
 </li>

diff --git a/docs/build/html/further-information/faq.html b/docs/build/html/further-information/faq.html
@@ -39,7 +39,7 @@
   <link rel="stylesheet" href="../_static/_templates/custom.css" type="text/css" />
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="About" href="about.html" />
+    <link rel="next" title="Uninstalling DICAST" href="uninstall-dicast.html" />
     <link rel="prev" title="Examples" href="example-files.html" /> 
 </head>
 
@@ -159,9 +159,8 @@
 <li class="toctree-l1"><a class="reference internal" href="example-files.html">Examples</a><ul class="simple">
 </ul>
 </li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">FAQ</a><ul class="simple">
-</ul>
-</li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">FAQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="uninstall-dicast.html">Uninstalling DICAST</a></li>
 <li class="toctree-l1"><a class="reference internal" href="about.html">About</a><ul class="simple">
 </ul>
 </li>
@@ -239,8 +238,6 @@ <h1>FAQ<a class="headerlink" href="#faq" title="Permalink to this headline">¶</
 </div>
 </dd>
 </dl>
-<div class="toctree-wrapper compound">
-</div>
 </div>
 
 
@@ -251,7 +248,7 @@ <h1>FAQ<a class="headerlink" href="#faq" title="Permalink to this headline">¶</
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="about.html" class="btn btn-neutral float-right" title="About" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="uninstall-dicast.html" class="btn btn-neutral float-right" title="Uninstalling DICAST" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
         <a href="example-files.html" class="btn btn-neutral float-left" title="Examples" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>