VEP cache/plugin directory option not implemented

ylab-hi / ScanNeo

A pipeline for identifying indel derived neoantigens using RNA-Seq data

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VEP cache/plugin directory option not implemented #13

Closed sandain closed 2 years ago

sandain commented 2 years ago

According to the README, there is an option to provide the location of the VEP cache/plugin directory for the indels annotation phase. However, this option is not currently implemented:

usage: ScanNeo.py [-h] [-v] {indel,anno,hla,fasta} ...
ScanNeo.py: error: unrecognized arguments: -d /mnt/store3/clustcrilab/tools/scanneo/vep/

usage: ScanNeo.py [-h] [-v] {indel,anno,hla,fasta} ...
ScanNeo.py: error: unrecognized arguments: --dir /mnt/store3/clustcrilab/tools/scanneo/vep/

dolittle007 commented 2 years ago

I have fixed this bug. 56fe1d9 Thanks a lot.

sandain commented 2 years ago

Thanks. I was working on a patch, but I'll revert my changes and use yours.