Update VEP runner to use Life Sciences API beta & VEP 104 #698
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@moschetti Please note this merge was blocked and it is much needed. |
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Also it seems the ftp path, reverted to small vep instead of caps |
pgrosu
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Nov 7, 2021
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@moschetti There does not exist a mouse_mm9, though there is a mus_musculus:
[pgrosu]$ gsutil ls gs://cloud-lifesciences/vep/
gs://cloud-lifesciences/vep/
gs://cloud-lifesciences/vep/vep_cache_homo_sapiens_GRCh37_104.tar.gz
gs://cloud-lifesciences/vep/vep_cache_homo_sapiens_GRCh37_91.tar.gz
gs://cloud-lifesciences/vep/vep_cache_homo_sapiens_GRCh38_104.tar.gz
gs://cloud-lifesciences/vep/vep_cache_homo_sapiens_GRCh38_91.tar.gz
gs://cloud-lifesciences/vep/vep_cache_mus_musculus_GRCm39_104.tar.gz
[pgrosu]$
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@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. |
these are being updated because this branch updates to use VEP 104 from 91 so there are different annotations included
Moschetti/vepversioning
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--locationflagI will re-run tests after the variant-annotation updates and the new container push.
Fixes #650, #655, #665