NAME

shelf - Search for HPC packages in the cluster

VERSION

version 0.12.0

SYNOPSIS

            

              
              
shelf [options] search_key
            
          

DESCRIPTION

Scan installed packages in the NBI HPC. The search is case insensitive. Will use a cache file to speed up the search.

OPTIONS

-l, --legacy-only

Only display software in the legacy catalogue.

-n, --new-only

Only display software in the new catalogue (containers).

--refresh

Force a refresh of the cache file.

--verbose

Prints more information about the packages.

--version

Prints the version of the script.

OUTPUT

When searching for a query string, the script will print the name and how to activate it:

            

              
              
shelf metaphlan
            
          

Will produce:

            

              
              
MetaPhlAn               source package 9020df39-c4ad-402b-b299-896159114bd7 
metaphlan2-2.7.5        source package /nbi/software/testing/bin/metaphlan2-2.7.5 
metaphlan-3.0           source package /ei/software/testing/bin/metaphlan-3.0 
metaphlan-2f1b17a1f4e9  source package /ei/software/testing/bin/metaphlan-2f1b17a1f4e9 
metaphlan2-2.96.1       source package /ei/software/testing/bin/metaphlan2-2.96.1 
MetaPhlAn               source package edb34606-aeeb-41c2-890b-079c2ef1fd1c 
metaphlan-3.0.13        source package /nbi/software/testing/bin/metaphlan-3.0.13 
metaphlan-2.0           source package /ei/software/testing/bin/metaphlan-2.0 
metaphlan2-2.7.8        source package /nbi/software/testing/bin/metaphlan2-2.7.8
            
          

When a singularity package ID is specified, if a manifest is found it will print the details:

            

              
              
shelf 9020df39-c4ad-402b-b299-896159114bd7
            
          

Will produce:

            

              
              
== MetaPhlAn 3.0.10 == (QIB)  
Provides: 
 - metahplan  
 - read_fastx.py  
 - merge_metaphlan_tables.py  
Description: MetaPhlAn is a computational tool for profiling the composition of microbial communities
(Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.
With StrainPhlAn 3.0, it is possible to perform accurate strain-level microbial profiling.
[https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0]  
Build date: UNK  
  
source package 9020df39-c4ad-402b-b299-896159114bd7
            
          

AUTHOR

Andrea Telatin <proch@cpan.org>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2023-2025 by Andrea Telatin.

This is free software, licensed under:

            

              
              
The MIT (X11) License