docs: updated software list

stanford-rc · Oct 24, 2023 · 3d19939 · 3d19939
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diff --git a/includes/data/software.yml b/includes/data/software.yml
@@ -853,12 +853,10 @@ software_modules:
       versions:
       - {description: 'LibreSSL is a version of the TLS/crypto stack forked from OpenSSL
           in 2014, with goals of modernizing the codebase, improving security, and
-          applying best practice development processes.', family: ssl, markedDefault: false,
-        versionName: 2.5.3}
+          applying best practice development processes.', markedDefault: false, versionName: 2.5.3}
       - {description: 'LibreSSL is a version of the TLS/crypto stack forked from OpenSSL
           in 2014, with goals of modernizing the codebase, improving security, and
-          applying best practice development processes.', family: ssl, markedDefault: false,
-        versionName: 3.2.1}
+          applying best practice development processes.', markedDefault: false, versionName: 3.2.1}
     - categories: system, file management
       defaultVersionName: 0.9.3
       description: fpart sorts files and packs them into partitions.
@@ -1909,7 +1907,7 @@ software_modules:
       url: https://www.openssl.org/
       versions:
       - {description: OpenSSL is a full-featured toolkit for general-purpose cryptography
-          and secure communication., family: ssl, markedDefault: false, versionName: 3.0.7}
+          and secure communication., markedDefault: false, versionName: 3.0.7}
     - categories: system, libs
       defaultVersionName: 1.8.2
       description: Libgcrypt is a general purpose cryptographic library originally
@@ -4379,13 +4377,13 @@ software_modules:
       - {description: Python API for comprehensive GWAS analysis using GEMMA., markedDefault: false,
         versionName: 0.8.9_py39}
     - categories: biology, cryo-em
-      defaultVersionName: '2.1'
+      defaultVersionName: 4.0.1
       description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on)
         is a 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).
       package: relion
-      url: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page
+      url: https://github.com/3dem/relion
       versions:
       - description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on)
           is a stand-alone computer program that employs an empirical Bayesian approach
@@ -4405,6 +4403,15 @@ software_modules:
           arch: {gpu: 1}
           parallel: {mpi: 1}
         versionName: '2.1'
+      - description: RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on)
+          is a 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).
+        markedDefault: false
+        properties:
+          arch: {gpu: 1}
+          parallel: {mpi: 1}
+        versionName: 4.0.1
     - categories: biology, genomics
       defaultVersionName: 2.10.0
       description: 'HiC-Pro: An optimized and flexible pipeline for Hi-C data processing.'

diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml
@@ -5,6 +5,15 @@
 <description>Sherlock software update feed</description>
 <link>https://www.sherlock.stanford.edu/docs/software/list</link>
 <atom:link href="https://www.sherlock.stanford.edu/docs/software/updates.xml" rel="self" type="application/rss+xml"/>
+    <item>
+        <title>New version: biology/relion version 4.0.1</title>
+        <description>RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a 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).</description>
+        <link>https://github.com/3dem/relion</link>
+        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.0.1#relion</guid>
+        <category>biology, cryo-em</category>
+        <author>[email protected] (Kilian Cavalotti)</author>
+        <pubDate>Tue, 24 Oct 2023 16:24:43 -0700</pubDate>
+    </item>
     <item>
         <title>New module: devel/code-server version 4.16.1</title>
         <description>Run VS Code on any machine anywhere and access it in the browser.</description>
@@ -194,41 +203,5 @@
         <author>[email protected] (Kilian Cavalotti)</author>
         <pubDate>Fri, 18 Aug 2023 13:56:51 -0700</pubDate>
     </item>
-    <item>
-        <title>New module: system/jansson version 2.13.1</title>
-        <description>C library for encoding, decoding and manipulating JSON data.</description>
-        <link>https://github.com/akheron/jansson</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.13.1#jansson</guid>
-        <category>system, libs</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Mon, 14 Aug 2023 08:29:17 -0700</pubDate>
-    </item>
-    <item>
-        <title>New module: physics/swash version 9.01a</title>
-        <description>SWASH (an acronym of Simulating WAves till SHore) is a non-hydrostatic wave-flow model.</description>
-        <link>https://swash.sourceforge.io/</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=9.01a#swash</guid>
-        <category>physics, geoscience</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Thu, 20 Jul 2023 17:09:20 -0700</pubDate>
-    </item>
-    <item>
-        <title>New module: biology/py-vcf2gwas version 0.8.9_py39</title>
-        <description>Python API for comprehensive GWAS analysis using GEMMA.</description>
-        <link>https://github.com/frankvogt/vcf2gwas</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.8.9_py39#py-vcf2gwas</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Mon, 17 Jul 2023 18:23:53 -0700</pubDate>
-    </item>
-    <item>
-        <title>New module: biology/gemma version 0.98.5</title>
-        <description>GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.</description>
-        <link>https://github.com/genetics-statistics/GEMMA</link>
-        <guid>https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.98.5#gemma</guid>
-        <category>biology, genomics</category>
-        <author>[email protected] (Kilian Cavalotti)</author>
-        <pubDate>Mon, 17 Jul 2023 18:23:37 -0700</pubDate>
-    </item>
 </channel>
 </rss>