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habrok:software_environment:module_system [2023/03/21 12:59] – adminhabrok:software_environment:module_system [2025/08/28 09:15] (current) – [module overview] pedro
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 ====== Software environment ====== ====== Software environment ======
  
-On Hábrók a lot of software has been made available. In order to allow multiple versions of software to be available the software is arranged in so-called modules.+On Hábrók a lot of software has been made available using the [[https://easybuild.io/|EasyBuild software installation framework]]. In order to allow multiple versions of software to be available the software is arranged in so-called modules.
  
 ===== module system ===== ===== module system =====
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 The subcommands are: 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   * ''load'' or ''add'' for loading software into the environment
   * ''list'' for showing the currently loaded modules   * ''list'' for showing the currently loaded modules
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 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.  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> <code>
 [username@habrok ~]$ module avail r/4 [username@habrok ~]$ module avail r/4
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 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. 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 ==== ==== module load/add ====