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@stevenvdb stevenvdb commented Jan 31, 2024

(created using eb --new-pr)

As discussed previously (#3017, easybuilders/easybuild-easyconfigs#17340, Ensembl/ensembl-vep#1364), installing VEP with --SPECIES all gives errors (even in the most recent VEP versions). This PR only installs one specific specie.

To be honest, I am not entirely sure which species to choose, I guess users can download the ones they need afterwards if necessary.

This goes together with easybuilders/easybuild-easyconfigs#19763

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ocaisa commented Feb 1, 2024

This has been tested in easybuilders/easybuild-easyconfigs#19763 (comment)

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LGTM

[install_step method]
applying regex substitutions to file(s): INSTALL.pl
  * regex pattern 'ftp://', replacement string 'https://'
  running command "perl -MConfig -e 'print $Config::Config{PERL_API_REVISION}'"
  (in /home/alanc/.local/easybuild/software/VEP/111-GCC-12.2.0/VEP-111)
  export PERLLIB='/home/alanc/.local/easybuild/software/VEP/111-GCC-12.2.0/modules/api:'
  running command "perl INSTALL.pl --NO_BIOPERL --NO_HTSLIB --AUTO af --SPECIES cyprinus_carpio_carpio --NO_UPDATE --DESTDIR /home/alanc/.local/easybuild/software/VEP/111-GCC-12.2.0/modules/api"
  (in /home/alanc/.local/easybuild/software/VEP/111-GCC-12.2.0/VEP-111)

@ocaisa ocaisa merged commit 3df2035 into easybuilders:develop Feb 1, 2024
@migueldiascosta migueldiascosta added this to the 4.9.1 milestone Apr 4, 2024
@migueldiascosta migueldiascosta changed the title Install only selected species in VEP add species easyconfig parameter to VEP easyblock Apr 4, 2024
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3 participants