Deploy to GitHub Pages: 5b2c460

Installed_Software_Lists/module-packages/index.html

@@ -1222,7 +1222,7 @@ <h1 id="general-software-lists">General Software Lists<a class="headerlink" href
 <p>Our clusters have a wide range of software installed, available by using the modules system.</p>
 <p>The module files are organised by name, version, variant (where applicable) and, if relevant, the compiler version used to build the software. If no compiler version is given, either no compiler was required, or only the base system compiler (<code>/usr/bin/gcc</code>) and libraries were used.</p>
 <p>When we install applications, we try to install them on all of our clusters, but sometimes licence restrictions prevent it. If something seems to be missing, it may be because we are not able to provide it. Please contact us for more information if this is hindering your work.</p>
-<p>The lists below were last updated at 12:35:11 (+0100) on 06 Jun 2023, and are generated from the software installed on the <a href="../../Clusters/Myriad/">Myriad</a> cluster.</p>
+<p>The lists below were last updated at 14:35:22 (+0100) on 06 Jun 2023, and are generated from the software installed on the <a href="../../Clusters/Myriad/">Myriad</a> cluster.</p>
 <h2 id="bundles">Bundles<a class="headerlink" href="#bundles" title="Permanent link">§</a></h2>
 <p>Some applications or tools depend on a lot of other modules, or have some awkward requirements. For these, we sometimes make a "bundle" module in this section, that loads all the dependencies.</p>
 <p>For Python and R in particular, we also have <code>recommended</code> bundles that load the module for a recent version of Python or R, along with a collection of packages for it that have been requested by users, and the modules those packages require.</p>
@@ -4961,6 +4961,10 @@ <h2 id="development-tools">Development Tools<a class="headerlink" href="#develop
 <td align="left">adds Git 2.32.0 to your environment variables</td>
 </tr>
 <tr>
+<td align="center"><code>git/2.41.0-lfs-3.3.0</code></td>
+<td align="left">Git is a free and open source distributed version control system. This installation includes git-lfs pre-configured.</td>
+</tr>
+<tr>
 <td align="center"><code>gperf/3.0.4/gnu-4.9.2</code></td>
 <td align="left">Adds gperf 3.0.4 to your environment. GNU gperf is a perfect hash function generator.</td>
 </tr>

Installed_Software_Lists/python-packages/index.html

@@ -1096,7 +1096,7 @@ <h1 id="python-packages">Python Packages<a class="headerlink" href="#python-pack
 
 <p>The version of Python 3 provided with this bundle is currently Python 3.9.10.</p>
 <p>Note that some packages we do not provide this way, because they have complicated non-Python dependencies. These are usually provided using the normal application modules system. This includes <strong>TensorFlow</strong>.</p>
-<p>The following list was last updated at 12:35:03 (+0100) on 06 Jun 2023.</p>
+<p>The following list was last updated at 14:35:03 (+0100) on 06 Jun 2023.</p>
 <table>
 <thead>
 <tr>

Installed_Software_Lists/r-packages/index.html

@@ -1095,7 +1095,7 @@ <h1 id="r-packages">R Packages<a class="headerlink" href="#r-packages" title="Pe
 </code></pre></div>
 
 <p>The version of R provided with this bundle is currently R version 4.2.0 (2022-04-22).</p>
-<p>The following list was last updated at: 12:35:06 (+0100) on 06 Jun 2023.</p>
+<p>The following list was last updated at: 14:35:17 (+0100) on 06 Jun 2023.</p>
 <table>
 <thead>
 <tr>

Software_Guides/Other_Software/index.html

@@ -1290,6 +1290,13 @@
       </ul>
     </nav>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nextflow" class="md-nav__link">
+    Nextflow
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -1888,6 +1895,13 @@
       </ul>
     </nav>
 
+</li>
+
+          <li class="md-nav__item">
+  <a href="#nextflow" class="md-nav__link">
+    Nextflow
+  </a>
+
 </li>
 
           <li class="md-nav__item">
@@ -2915,6 +2929,10 @@ <h4 id="mpi">MPI<a class="headerlink" href="#mpi" title="Permanent link">§</a><
 gerun namd2 apoa1.namd 
 </code></pre></div>
 
+<h3 id="nextflow">Nextflow<a class="headerlink" href="#nextflow" title="Permanent link">§</a></h3>
+<p>We do not currently have central installs of Nextflow, but a group of UCL researchers have 
+contributed a config file and instructions for Myriad at the <a href="https://github.com/nf-core/configs/blob/master/docs/ucl_myriad.md">nf-core/configs repository</a></p>
+<p>Nextflow containers can be run using <a href="../Singularity.md">Singularity</a>.</p>
 <h3 id="nonmem">NONMEM<a class="headerlink" href="#nonmem" title="Permanent link">§</a></h3>
 <p>NONMEM® is a nonlinear mixed effects modelling tool used in population pharmacokinetic / pharmacodynamic analysis. </p>
 <p>We have one build that uses the GNU compiler and ATLAS and an Intel build using MKL. Both use Intel MPI. </p>