Updated installation docs

FCP-INDI · Nov 6, 2015 · 22f6da0 · 22f6da0
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diff --git a/docs/user/_sources/install.txt b/docs/user/_sources/install.txt
@@ -107,6 +107,8 @@ Please ensure that you are using Python 2.7 and above, but not Python 3 (since i
 * `iPython <http://ipython.org/>`_ (optional)
 * `PyGraphviz <http://www.graphviz.org/>`_ (optional; required for workflow graphs)
 * `Patsy <https://patsy.readthedocs.org/en/latest/>`_
+* `Boto 3 <https://boto3.readthedocs.org/en/latest/>`_
+* `psutil <https://github.com/giampaolo/psutil>`_
 
 Miniconda
 """"""""
@@ -123,7 +125,7 @@ The following commands will install all the Python dependencies within a Minicon
    conda create -y -n cpac python
    source activate cpac
    conda install -y cython numpy scipy matplotlib networkx traits pyyaml jinja2 nose ipython pip wxpython
-   pip install lockfile pygraphviz nibabel nipype patsy
+   pip install lockfile pygraphviz nibabel nipype patsy psutil boto3
    source deactivate
 
 OS-Specific Instructions 
@@ -177,7 +179,8 @@ OS-Specific Instructions
     apt-get update
 
 * FSL : ``apt-get install -y fsl-5.0-complete``
-* AFNI : ``apt-get install -y afni``
+
+We have encountered compatibility issues in the past with the Neurodebian binary for AFNI.  For this reason, it is suggested that you follow the official installation instructions from the AFNI homepage (see above).
 
 **Mac OS X:**
 

diff --git a/docs/user/install.html b/docs/user/install.html
@@ -6,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>Installing C-PAC &mdash; C-PAC 0.3.9 Alpha documentation</title>
+    <title>Installing C-PAC &mdash; C-PAC 0.4.0 Alpha documentation</title>
 
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
 
     <script type="text/javascript">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.3.9 Alpha',
+        VERSION:     '0.4.0 Alpha',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true
@@ -24,7 +24,7 @@
     <script type="text/javascript" src="_static/underscore.js"></script>
     <script type="text/javascript" src="_static/doctools.js"></script>
     <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="top" title="C-PAC 0.3.9 Alpha documentation" href="index.html" />
+    <link rel="top" title="C-PAC 0.4.0 Alpha documentation" href="index.html" />
     <link rel="next" title="Using C-PAC" href="use.html" />
     <link rel="prev" title="Welcome to C-PAC’s Documentation!" href="index.html" /> 
   </head>
@@ -41,7 +41,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to C-PAC’s Documentation!"
              accesskey="P">previous</a> |</li>
-        <li><a href="index.html">C-PAC 0.3.9 Alpha documentation</a> &raquo;</li> 
+        <li><a href="index.html">C-PAC 0.4.0 Alpha documentation</a> &raquo;</li> 
       </ul>
     </div>  
 
@@ -156,6 +156,8 @@ <h2>Installing Python Dependencies<a class="headerlink" href="#installing-python
 <li><a class="reference external" href="http://ipython.org/">iPython</a> (optional)</li>
 <li><a class="reference external" href="http://www.graphviz.org/">PyGraphviz</a> (optional; required for workflow graphs)</li>
 <li><a class="reference external" href="https://patsy.readthedocs.org/en/latest/">Patsy</a></li>
+<li><a class="reference external" href="https://boto3.readthedocs.org/en/latest/">Boto 3</a></li>
+<li><a class="reference external" href="https://github.com/giampaolo/psutil">psutil</a></li>
 </ul>
 <div class="section" id="id1">
 <h3>Miniconda<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
@@ -168,7 +170,7 @@ <h3>Miniconda<a class="headerlink" href="#id1" title="Permalink to this headline
 conda create -y -n cpac python
 <span class="nb">source </span>activate cpac
 conda install -y cython numpy scipy matplotlib networkx traits pyyaml jinja2 nose ipython pip wxpython
-pip install lockfile pygraphviz nibabel nipype patsy
+pip install lockfile pygraphviz nibabel nipype patsy psutil boto3
 <span class="nb">source </span>deactivate
 </pre></div>
 </div>
@@ -217,9 +219,8 @@ <h3>OS-Specific Instructions<a class="headerlink" href="#id6" title="Permalink t
 </li>
 <li><p class="first">FSL : <tt class="docutils literal"><span class="pre">apt-get</span> <span class="pre">install</span> <span class="pre">-y</span> <span class="pre">fsl-5.0-complete</span></tt></p>
 </li>
-<li><p class="first">AFNI : <tt class="docutils literal"><span class="pre">apt-get</span> <span class="pre">install</span> <span class="pre">-y</span> <span class="pre">afni</span></tt></p>
-</li>
 </ul>
+<p>We have encountered compatibility issues in the past with the Neurodebian binary for AFNI.  For this reason, it is suggested that you follow the official installation instructions from the AFNI homepage (see above).</p>
 <p><strong>Mac OS X:</strong></p>
 <ul class="simple">
 <li>FSL - Follow the instructions on the <a class="reference external" href="http://fsl.fmrib.ox.ac.uk/fsldownloads/fsldownloadmain.html">FSL Download Page</a>.</li>
@@ -407,7 +408,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to C-PAC’s Documentation!"
              >previous</a> |</li>
-        <li><a href="index.html">C-PAC 0.3.9 Alpha documentation</a> &raquo;</li> 
+        <li><a href="index.html">C-PAC 0.4.0 Alpha documentation</a> &raquo;</li> 
       </ul>
     </div>
     <div class="footer">