GeneSplicer: improve argument processing

[nuno-agostinho]

Improves on Ensembl/ensembl-vep#1599

Changelog

• Accept genesplicer command instead of a path
  • Works if genesplicer is exported in the $PATH variable (like in VEP Docker)
  • Path to genesplicer is internally obtained via which
• Add key-value params to first two positional arguments:
  • binary with genesplicer as default
  • training with no default
• Improve plugin docs
  • Add information on how to use GeneSplicer with VEP Docker/Singularity

Testing

If genesplicer is exported in the $PATH variable, like in VEP Docker/Singularity (Ensembl/ensembl-vep#1599), there is no need to explicitly call it:

vep --id rs1348242192 --database --force --plugin GeneSplicer,training=${human_data}

This means that the only mandatory argument now is the training data.

[olaaustine]

Hi @nuno-agostinho,
Thank you very much for this change, tested while running on docker v4.27.1
Just some changes.
Thank you
Ola

[nuno-agostinho]

Hi @olaaustine, I updated the PR with your suggestions. Thanks!

[olaaustine]

Hi @nuno-agostinho,
Thank you for this change.
Tested on Docker and on the cluster.
LGTM!.
Waiting for this before merging.
Thank you

[olaaustine]

Merged into release/112 and main.