Deploy preview for PR 32 🛫

Author: tefarley

pr-preview/pr-32/admin/ondemand/index.html

@@ -2174,7 +2174,7 @@ <h2 id="admin-troublshooting">Admin Troublshooting<a class="headerlink" href="#a
 </ol>
 <p>Apache then starts an NginX server as the user and most things like the main dashboard, submitting jobs, running apps, etc happen here in the PUN. Any errors encountered at this step will be in the logs at <code>/var/log/ondemand-nginx/$user/error.log</code>. You can also see what might be happening here by running commands like <code>ps aux | grep $USER</code> to see the users PUN, or <code>ps aux | grep -i nginx</code> to see all the PUNs. From the ondemand web UI theres an option to "Restart Web Server" which essentially kills and restarts the users PUN.</p>
 <ol>
-<li>/pun/sys/dashboard</li>
+<li>Dashboard (https://localhost/pun/sys/dashboard)</li>
 </ol>
 <p>The dashboard is mostly covered in section 4, but just wanted to denote that apache then redirects us here after the PUN has been started where users can do everything else. At this step OOD will warn you about things like "Home Directory Not Found" and such. If you get this far I'd recommend you troubleshoot issues with users' home dir, NASii, and free space: <code>df | grep $HOME</code>, <code>du -sh $HOME</code>, <code>journalctl -u  autofs</code>, and umount stuff. Check that <code>$HOME/ondemand</code> exists perhaps.</p>
 <ol>

pr-preview/pr-32/franklin/software/modules/index.html

@@ -3825,7 +3825,7 @@ <h3 id="corset">corset<a class="headerlink" href="#corset" title="Permanent link
 <h3 id="ctffind">ctffind<a class="headerlink" href="#ctffind" title="Permanent link">&para;</a></h3>
 <p>Fast and accurate defocus estimation from electron micrographs.</p>
 <p><strong>Versions</strong>: 4.1.14</p>
-<p><strong>Arches</strong>: amd, intel</p>
+<p><strong>Arches</strong>: intel, amd</p>
 <p><strong>Modules</strong>: <code>ctffind/4.1.14+intel</code>, <code>ctffind/4.1.14+amd</code></p>
 <h3 id="cuda">cuda<a class="headerlink" href="#cuda" title="Permanent link">&para;</a></h3>
 <p>CUDA is a parallel computing platform and programming model invented by
@@ -3834,7 +3834,7 @@ <h3 id="cuda">cuda<a class="headerlink" href="#cuda" title="Permanent link">&par
 package does not currently install the drivers necessary to run CUDA.
 These will need to be installed manually. See:
 https://docs.nvidia.com/cuda/ for details.</p>
-<p><strong>Versions</strong>: 11.8.0, 11.7.1</p>
+<p><strong>Versions</strong>: 11.7.1, 11.8.0</p>
 <p><strong>Arches</strong>: generic</p>
 <p><strong>Modules</strong>: <code>cuda/11.8.0</code>, <code>cuda/11.7.1</code></p>
 <h3 id="cufflinks">cufflinks<a class="headerlink" href="#cufflinks" title="Permanent link">&para;</a></h3>
@@ -3891,7 +3891,7 @@ <h3 id="freebayes">freebayes<a class="headerlink" href="#freebayes" title="Perma
 <h3 id="gatk">gatk<a class="headerlink" href="#gatk" title="Permanent link">&para;</a></h3>
 <p>Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing
 Data</p>
-<p><strong>Versions</strong>: 3.8.1, 4.2.6.1</p>
+<p><strong>Versions</strong>: 4.2.6.1, 3.8.1</p>
 <p><strong>Arches</strong>: generic</p>
 <p><strong>Modules</strong>: <code>gatk/3.8.1</code>, <code>gatk/4.2.6.1</code></p>
 <h3 id="gcc">gcc<a class="headerlink" href="#gcc" title="Permanent link">&para;</a></h3>
@@ -4354,9 +4354,9 @@ <h3 id="relion">relion<a class="headerlink" href="#relion" title="Permanent link
 stand-alone computer program that employs an empirical Bayesian approach
 to refinement of (multiple) 3D reconstructions or 2D class averages in
 electron cryo-microscopy (cryo-EM).</p>
-<p><strong>Versions</strong>: 3.1.3, 4.0.1, 4.0.0</p>
+<p><strong>Versions</strong>: 4.0.0, 3.1.3, 4.0.1</p>
 <p><strong>Variants</strong>: gpu, cpu</p>
-<p><strong>Arches</strong>: intel+gpu_delay, amd, intel</p>
+<p><strong>Arches</strong>: intel+gpu_delay, intel, amd</p>
 <p><strong>Modules</strong>: <code>relion/cpu/3.1.3+amd</code>, <code>relion/gpu/3.1.3+amd</code>, <code>relion/gpu/3.1.3+intel</code>, <code>relion/cpu/4.0.0+amd</code>, <code>relion/gpu/4.0.0+amd</code>, <code>relion/gpu/4.0.0+intel</code>, <code>relion/3.1.3</code>, <code>relion/4.0.0</code>, <code>relion/cpu/4.0.1+amd</code>, <code>relion/gpu/4.0.1+amd</code>, <code>relion/4.0.1</code>, <code>relion/gpu/4.0.1+intel+gpu_delay</code>, <code>relion/gpu/4.0.1+intel</code></p>
 <h3 id="relion-bbr">relion-bbr<a class="headerlink" href="#relion-bbr" title="Permanent link">&para;</a></h3>
 <p>A modified version of Relion supporting block-based-reconstruction as
@@ -4367,7 +4367,7 @@ <h3 id="relion-bbr">relion-bbr<a class="headerlink" href="#relion-bbr" title="Pe
 <p><strong>Modules</strong>: <code>relion-bbr/gpu/3.1.2+intel</code></p>
 <h3 id="relion-helper">relion-helper<a class="headerlink" href="#relion-helper" title="Permanent link">&para;</a></h3>
 <p>Utilities for Relion Cryo-EM data processing on clusters.</p>
-<p><strong>Versions</strong>: 0.2, 0.1, 0.3</p>
+<p><strong>Versions</strong>: 0.1, 0.2, 0.3</p>
 <p><strong>Arches</strong>: generic</p>
 <p><strong>Modules</strong>: <code>relion-helper/0.1</code>, <code>relion-helper/0.2</code>, <code>relion-helper/0.3</code></p>
 <h3 id="repeatmasker">repeatmasker<a class="headerlink" href="#repeatmasker" title="Permanent link">&para;</a></h3>