https://wiki.anunna.wur.nl/index.php?action=history&feed=atom&title=Software_Overview 2026-08-09T14:54:44Z Revision history for this page on the wiki MediaWiki 1.45.3 https://wiki.anunna.wur.nl/index.php?title=Software_Overview&diff=2949&oldid=prev 2026-06-19T20:35:28Z

<p>Link ABGC/JBrowse from See also (orphan fix) (via update-page on MediaWiki MCP Server)</p> <table style="background-color: #fff; color: #202122;" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:35, 19 June 2026</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l38">Line 38:</td> <td colspan="2" class="diff-lineno">Line 38:</td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Licensed Software]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Licensed Software]]</div></td></tr> <tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Requesting New Software]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [[Requesting New Software]]</div></td></tr> <tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [[ABGC/JBrowse]] — setting up JBrowse (ABGC genome browser)</ins></div></td></tr> </table>

Haars001 https://wiki.anunna.wur.nl/index.php?title=Software_Overview&diff=2785&oldid=prev 2026-06-16T14:31:16Z

<p>Phase 1 § 5 P1.5.1 / Phase 2 P2.9: software landscape hub. Note: General overview NOT consumed here (it is GUI/OOD content reserved for § 7 Portal Overview); Modules content already lives in Environment Modules. (via create-page on MediaWiki MCP Server)</p> <p><b>New page</b></p><div>Anunna offers software in several ways, depending on whether you need a ready-made package, your own custom setup, or a commercial product. This page is a map of the options and points to the page that covers each in detail.<br /> <br /> == Pre-installed software: modules ==<br /> <br /> Most software on the cluster is provided as [[Environment Modules | environment modules]], organised into yearly &quot;buckets&quot;. Load a bucket and then the software you need — the module sets up your environment so the right versions of the program and its dependencies are available. Use &lt;code&gt;module key &lt;name&gt;&lt;/code&gt; to search for a package, and request additions through [[Requesting New Software]].<br /> <br /> == Languages ==<br /> <br /> The common scientific languages have their own pages covering the provided modules, how to manage packages, and how to run them in jobs and notebooks:<br /> <br /> * [[Python]] — modules, virtual environments, Miniforge, and Jupyter kernels.<br /> * [[R]] — modules, local package libraries, batch jobs, and parallel R.<br /> * [[Julia]] — modules and package management.<br /> <br /> == Your own software ==<br /> <br /> If a package is not available as a module, you have a few options:<br /> <br /> * [[Installing Personal Software]] — shell configuration, environment variables, and installing small tools into your own space.<br /> * [[Apptainer]] — package an application and all its dependencies into a portable container. This is the most reproducible way to bring in software that is awkward to install directly.<br /> <br /> == Commercial and licensed software ==<br /> <br /> Some packages are commercial and restricted to eligible users — see [[Licensed Software]] for what is available and how to get access.<br /> <br /> == Graphical applications ==<br /> <br /> Several applications are available through your web browser via the Apps Portal, without using the command line — see [[General overview | the Apps Portal overview]].<br /> <br /> == Requesting new software ==<br /> <br /> If what you need is not available anywhere above, [[Requesting New Software | submit a software request]].<br /> <br /> == See also ==<br /> <br /> * [[Environment Modules]]<br /> * [[Installing Personal Software]]<br /> * [[Licensed Software]]<br /> * [[Requesting New Software]]</div>

Haars001