New software installed: VEP version 110

Major Edit

After facing to some error to install plugins on this tools I open a ticket on the maintainers’s github of vep.

They recommand to use the singularity instance for each user:

Please follow this procedure to install VEP:

https://doc.eresearch.unige.ch/hpc/applications_and_libraries#variant_effect_predictor_vep

As Module VEP is non fully functionnal it will be erased from clusters

Decapreted Post:


Dear users, we have installed a new software: VEP 110:


---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
  VEP: VEP/110
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory
      regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP.


    You will need to load all module(s) on any one of the lines below before the "VEP/110" module is available to load.

      GCC/11.3.0
 
    Help:
      Description
      ===========
      Variant Effect Predictor (VEP) determines the effect of your
       variants (SNPs, insertions, deletions, CNVs or structural variants) on genes,
       transcripts, and protein sequence, as well as regulatory regions.
       Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently
       used routines in VEP.
      
      
      More information
      ================
       - Homepage: https://www.ensembl.org/info/docs/tools/vep
      
      
      Included extensions
      ===================
      Bio::EnsEMBL::XS-2.3.2
      


 

Best,
HPC team

Plugin Installation

@Alexander.Couzens
If you require a plugin, you can install it by loading the module and then executing the following command line interface (CLI):

perl /opt/ebsofts/VEP/110-GCC-11.3.0/INSTALL.pl -a p -g <plugin_name>

1 Like

Hi @Alexander.Couzens

I’ve updated this post according to the ensembl maintainers’ recommendations.

Could you try this installation and let me know if it works for you?