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--- habrok:software_environment:module_system [2025/04/25 08:57] – admin
+++ habrok:software_environment:module_system [2025/08/28 09:15] (current) – [module overview] pedro
@@ Line 17: / Line 17: @@
 The subcommands are:
-  * ''avail'' for showing a list of available software
+  * ''avail'' for showing an exhaustive list of available software
+  * ''overview'' for showing a concise list of available software
   * ''load'' or ''add'' for loading software into the environment
   * ''list'' for showing the currently loaded modules
@@ Line 51: / Line 52: @@
 We can use the spacebar to scroll through the extensive list. As you can see the list contains software packages. For each package one or more versions is available.
-In order to bring down the list to certain packages only we can specify an argument to ''module avail''. If we specify 'R', or 'r' as an argument it will show us all packages with an 'r' in its name. This will not help much, so we have to be more precise. A more useful search string would be 'r/3':
+In order to bring down the list to certain packages only we can specify an argument to ''module avail''. If we specify 'R', or 'r' as an argument it will show us all packages with an 'r' in its name. This will not help much, so we have to be more precise. A more useful search string would be 'r/4':
 <code>
 [username@habrok ~]$ module avail r/4
@@ Line 67: / Line 68: @@
 Now we can see the actual version(s) of R that is/are available. If multiple versions of the same application are available, only one of them will have '(D)' behind the name, denoting that this is the default versions.
+==== module overview ====
+As we could see above, the ''module avail'' command and subcommand return a very long and exhaustive list of all the installed software on Hábrók, which can be narrowed down with a particular search term. This can be very useful if one is interested in looking up all software or versions of a particular software, but the output is long and unwieldy. To simply list all available software regardless of version or the toolchain used to install them, the ''module overview'' command and subcommand are very useful:
+<code>
+[username@habrok ~]$ module overview
+--- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/ai ----
+ollama (2)   PyTorch-bundle (2)   PyTorch (8)
+--- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/astro ---
+astropy (1)
+--- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/bio ---
+AdapterRemoval      (1)   GDGraph       (2)    PhyloPhlAn            (1)
+ADMIXTURE           (1)   GeneMark-ET   (1)    phyx                  (1)
+AFNI                (1)   geNomad       (1)    picard                (2)
+AlphaFold           (1)   GenomeTools   (1)    PIPITS                (1)
+angsd               (1)   GetOrganelle  (3)    PLINK                 (3)
+ANIcalculator       (1)   GMAP-GSNAP    (1)    pplacer               (1)
+ARAGORN             (1)   GROMACS       (10)   PRANK                 (1)
+ASTER               (1)   GTDB-Tk       (1)    prodigal-gv           (2)
+ASTRAL              (1)   HH-suite      (1)    prodigal              (4)
+AUGUSTUS            (1)   HISAT2        (2)    prokka                (1)
+AutoDock-Vina       (1)   HMMER         (3)    PRSice                (1)
+BA3-SNPS-autotune   (1)   HTSeq         (1)    PSORTb                (1)
+... et cetera...
+</code>
+Here we can quickly see that, for instance, ''GROMACS''  is installed, with the number '10' in brackets corresponding to the total number of different installations available. Similarly to ''module avail'', we can narrow down our search to a particular module(s):
+<code>
+[username@habrok ~]$ module overview GROMACS
+--- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/bio ---
+GROMACS (10)
+</code>
 ==== module load/add ====