Move VEP files from a 110 path to GRCh38.
#844
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bpblanken
commented
Jul 24, 2024
| @@ -12,7 +12,7 @@ export PROJECT="$(gcloud config get-value project)" | |||
| export VEP_CONFIG_PATH="$(/usr/share/google/get_metadata_value attributes/VEP_CONFIG_PATH)" | |||
| export VEP_REPLICATE="$(/usr/share/google/get_metadata_value attributes/VEP_REPLICATE)" | |||
| export ASSEMBLY=GRCh38 | |||
| export VEP_DOCKER_IMAGE=gcr.io/seqr-project/vep-docker-image:110 | |||
| export VEP_DOCKER_IMAGE=gcr.io/seqr-project/vep-docker-image:GRCh38 | |||
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bblanken@wmbbe-67c seqr-loading-pipelines % docker pull gcr.io/seqr-project/vep-docker-image:GRCh38
GRCh38: Pulling from seqr-project/vep-docker-image
Digest: sha256:bc2dc75c1016f9cba2d39c91fcfd4c4f2098634f0b5585e2b0a0c7f8d069b4a8
Status: Image is up to date for gcr.io/seqr-project/vep-docker-image:GRCh38
gcr.io/seqr-project/vep-docker-image:GRCh38
also there.
hanars
approved these changes
Jul 24, 2024
bpblanken
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Aug 2, 2024
* Move vep files (#844) * Add mito local constraint (#845) * Add mito local constraint * Fix tests * lint * Benb/migration task (#834) * split import and validate * lint and share function * ruff * change dep * tweak update * lint * wrong method * correct method * mocks * change sample type annotation on test * hack on migration * sort return list * move the migration * still hacking * better! * getting there * Cleaner * ruff * Finish it off * migration * rename var * add migrations to annotations table * fix test import * actually fix the test * add migrations * not used here * use globals * missed one * a hilarious typo * Update migrate_variant_annotations_table.py * correct sign * add lookup migration * Add lookup table migration * adjust migration * ruff * Add to tasks * ensure a migration cannot run before a previous migration! * ruff * fix bug * lint * add referencegenomedatasetype * Annoying but fixed * Add new SV annotations for VCF export. (#857) * Add SV annotations * ruff * push * ruff * Update update_variant_annotations_table_with_new_samples_test.py * Add a task to export the SV annotations table to VCF. (#858) * Export VCF task * Fix test * lint * Resolve the assumption in the pipeline that remap/pedigree files are immutable. (#856) * add remap_pedigree hash * add func * all the imports * ruff * Fix it * support missing remap * ruff * ruff * ruff * tweak the type * tweak the type * Fix test * ruff * add remap pedigree hash * Explicit int32 * lint * Update io.py * ruff * lint * hash * Flappy test * wrong pedigree * bad colon * finish tests * add a test * add pedigree * Fix test
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In preparation for supporting GRCh37 on VEP 11190. This is cleaner anyways: