I am trying to add initialization scripts on AWS because I am getting an error while trying to run your Hail 0.1 pipeline (I know it is not supported, but still need that since 0.2 is not yet released on your website fully):
ERROR: HailException: could not open file: /vep/vep-gcloud-grch37.properties (No such file or directory) when ‘run_vep’ function is run:
vds = run_vep(vds, genome_version=args.genome_version, block_size=args.vep_block_size)
So, I suppose it is because VEP was not installed. Are there any scripts that I could use to set up environment not on Google Cloud or I should just manually install VEP (and other things, probably)?
I tried just running
But it fails since it can’t find another file: