Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add species easyconfig parameter to VEP easyblock #3121

Merged
merged 2 commits into from
Feb 1, 2024

Conversation

stevenvdb
Copy link

@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

@ocaisa
Copy link
Member

ocaisa commented Feb 1, 2024

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

Copy link
Member

@ocaisa ocaisa left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
47 checks passed
@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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants