Move vep files (#844)

Author: bpblanken

v03_pipeline/bin/vep-110-GRCh38.sh

@@ -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
 
 mkdir -p /vep_data
 
@@ -36,26 +36,26 @@ sleep 60
 sudo service docker restart
 
 # Copied from the repo at v03_pipeline/var/vep_config
-gcloud storage cp --billing-project $PROJECT gs://seqr-reference-data/vep/110/vep-${ASSEMBLY}.json $VEP_CONFIG_PATH
+gcloud storage cp --billing-project $PROJECT gs://seqr-reference-data/vep/GRCh38/vep-${ASSEMBLY}.json $VEP_CONFIG_PATH
 
 # Copied from the UTRAnnotator repo (https://github.com/ImperialCardioGenetics/UTRannotator/tree/master)
-gcloud storage cp --billing-project $PROJECT gs://seqr-reference-data/vep/110/uORF_5UTR_${ASSEMBLY}_PUBLIC.txt /vep_data/ &
+gcloud storage cp --billing-project $PROJECT gs://seqr-reference-data/vep/GRCh38/uORF_5UTR_${ASSEMBLY}_PUBLIC.txt /vep_data/ &
 
 # Raw data files copied from the bucket (https://console.cloud.google.com/storage/browser/dm_alphamissense;tab=objects?prefix=&forceOnObjectsSortingFiltering=false)
 # tabix -s 1 -b 2 -e 2 -f -S 1 AlphaMissense_hg38.tsv.gz
-gcloud storage cp --billing-project $PROJECT 'gs://seqr-reference-data/vep/110/AlphaMissense_hg38.tsv.*' /vep_data/ &
+gcloud storage cp --billing-project $PROJECT 'gs://seqr-reference-data/vep/GRCh38/AlphaMissense_hg38.tsv.*' /vep_data/ &
 
 gcloud storage cat --billing-project $PROJECT gs://seqr-reference-data/vep_data/loftee-beta/${ASSEMBLY}.tar | tar -xf - -C /vep_data/ &
 
 # Copied from ftp://ftp.ensembl.org/pub/release-110/variation/indexed_vep_cache/homo_sapiens_vep_110_${ASSEMBLY}.tar.gz
-gcloud storage cat --billing-project $PROJECT gs://seqr-reference-data/vep/110/homo_sapiens_vep_110_${ASSEMBLY}.tar.gz | tar -xzf - -C /vep_data/ &
+gcloud storage cat --billing-project $PROJECT gs://seqr-reference-data/vep/GRCh38/homo_sapiens_vep_110_${ASSEMBLY}.tar.gz | tar -xzf - -C /vep_data/ &
 
 # Generated with:
 # curl -O ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.${ASSEMBLY}.dna.primary_assembly.fa.gz > Homo_sapiens.${ASSEMBLY}.dna.primary_assembly.fa.gz
 # gzip -d Homo_sapiens.${ASSEMBLY}.dna.primary_assembly.fa.gz
 # bgzip Homo_sapiens.${ASSEMBLY}.dna.primary_assembly.fa
 # samtools faidx Homo_sapiens.${ASSEMBLY}.dna.primary_assembly.fa.gz
-gcloud storage cp --billing-project $PROJECT "gs://seqr-reference-data/vep/110/Homo_sapiens.${ASSEMBLY}.dna.primary_assembly.fa.*" /vep_data/ &
+gcloud storage cp --billing-project $PROJECT "gs://seqr-reference-data/vep/GRCh38/Homo_sapiens.${ASSEMBLY}.dna.primary_assembly.fa.*" /vep_data/ &
 docker pull ${VEP_DOCKER_IMAGE} &
 wait