add species easyconfig parameter to VEP easyblock#3121
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ocaisa merged 2 commits intoeasybuilders:developfrom Feb 1, 2024
Merged
add species easyconfig parameter to VEP easyblock#3121ocaisa merged 2 commits intoeasybuilders:developfrom
species easyconfig parameter to VEP easyblock#3121ocaisa merged 2 commits intoeasybuilders:developfrom
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ocaisa
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This has been tested in easybuilders/easybuild-easyconfigs#19763 (comment) |
ocaisa
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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)
species easyconfig parameter to VEP easyblock
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(created using
eb --new-pr)As discussed previously (#3017, easybuilders/easybuild-easyconfigs#17340, Ensembl/ensembl-vep#1364), installing VEP with
--SPECIES allgives 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