I’ve installed like so:
conda install ensembl-vep=105.0-0
And then installed the human cache like this:
vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep —CONVERT
But I can’t get it to run with any commands, e.g.
vep --dir_cache "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-105.0-0" \
-i "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf" \
-o "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/vep_output.txt”
This gives an error message about downloading caches:
IMPORTANT INFORMATION:
The VEP can read gene data from either a local cache or local/remote databases.
Or this one:
vep --cache \
-i "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf" \
-o "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/vep_output.txt”
This gives the error:
MSG: ERROR: Cache directory /mnt/gpfs/home/skgtmdf/.vep/homo_sapiens not found
I don’t suppose anyone would be able to point me in the right direction?
I found the answer. You need to add both --cache and --dir_cache arguments:
vep --cache --dir_cache "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-105.0-0" \
-i "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf" \
-o "/mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/vep_output.txt"