tweak path

bpblanken · bpblanken · commit b11d9b32c560 · 2024-09-07T14:36:02.000-04:00
diff --git a/v03_pipeline/bin/download_vep_data.bash b/v03_pipeline/bin/download_vep_data.bash
@@ -3,7 +3,7 @@
 set -eux
 
 REFERENCE_GENOME=$1
-VEP_DATA=/vep_data
+VEP_DATA=/seqr/vep_data
 
 case $REFERENCE_GENOME in
   GRCh38)
diff --git a/v03_pipeline/bin/vep b/v03_pipeline/bin/vep
@@ -3,7 +3,7 @@
 set -eux
 
 REFERENCE_GENOME=$1
-VEP_DATA=/vep_data
+VEP_DATA=/seqr/vep_data
 VEP_DOCKER_IMAGE="gcr.io/seqr-project/vep-docker-image"
 
 case $REFERENCE_GENOME in
diff --git a/v03_pipeline/lib/vep.py b/v03_pipeline/lib/vep.py
@@ -5,7 +5,7 @@
 from v03_pipeline.lib.model import DatasetType, ReferenceGenome
 
 VEP_CONFIG_URI = Template(
-    'file:///vep_data/$reference_genome/vep-$reference_genome.json',
+    'file:///seqr/vep_data/$reference_genome/vep-$reference_genome.json',
 )
 
 

Original file line number	Diff line number	Diff line change
`@@ -5,7 +5,7 @@`
`5`	`5`	`from v03_pipeline.lib.model import DatasetType, ReferenceGenome`
`6`	`6`
`7`	`7`	`VEP_CONFIG_URI = Template(`
`8`		`- 'file:///vep_data/$reference_genome/vep-$reference_genome.json',`
	`8`	`+ 'file:///seqr/vep_data/$reference_genome/vep-$reference_genome.json',`
`9`	`9`	`)`
`10`	`10`
`11`	`11`