Update VEP runner to use Life Sciences API beta & VEP 104

googlegenomics / gcp-variant-transforms

GCP Variant Transforms

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Update VEP runner to use Life Sciences API beta & VEP 104 #698

Closed moschetti closed 2 years ago

moschetti commented 3 years ago

Update vep_runner & tests to use Cloud LifeSciences API, including adding --location flag
Update defaults to use newest VEP release (104) (Underlying GCS & GCR updates in: https://github.com/googlegenomics/variant-annotation/pull/15)

I will re-run tests after the variant-annotation updates and the new container push.

Fixes #650, #655, #665

hnawar commented 2 years ago

@moschetti Please note this merge was blocked and it is much needed. Thanks

hnawar commented 2 years ago

Also it seems the ftp path, reverted to small vep instead of caps ftp://ftp.ensembl.org/pub/release-104/variation/vep/homo_sapiens_vep_104_GRCh38.tar.gz

moschetti commented 2 years ago

@hnawar we're working on as couple other fixes as well right now with a plan to cut a new release shortly with multiple fixes so this is on hold to merge until then.