Use gtf file from nightly load

manulera commented 1 year ago

Hi @kimrutherford

Currently, the file data/pombe_genome.gtf is not updated, it was created using this repository and committed to this repo.

In this comment, I mentioned to include running this script to generate the output in the nightly run. https://github.com/pombase/website/issues/2058#issuecomment-1681906133

Once the gtf file is include in the release, you can replace the code below in get_data.sh by the right path and uncomment.

# TODO
# curl -k path/to/gtf_file/in/nightly/release -o data/pombe_genome.gtf

manulera commented 10 months ago

Hi @kimrutherford just pinging this issue because of a qestion in the helpdesk. As is, the pombe_genome.gtf file has not been updated in a while. This is only used to transform the allele descriptions into transvar-like variants. I will update it by hand now anyway.

manulera commented 6 months ago

Hi @kimrutherford I have added an action to update it on demand to the repo. You can run it from github from the action panel:

https://github.com/manulera/pombase_gtf_file

This will commit the new pombe_genome.gtf file to the repository if it changed, and this can then be included in the allele_qc repo for transvar.

pombase / allele_qc

Use gtf file from nightly load #108