Cannot run VEP when specifying gtf about ensembl-vep HOT 4 CLOSED

Strange.

I don't find that revision string to match any commit hash, can you be more specific? What is the version given when you run:

perl vep.pl

?

The code should catch this, but do you have Bio::DB::HTS installed? You can test with:

perl -MBio::DB::HTS::Tabix -e'print "OK\n"'

from ensembl-vep.

Hi Will,

Thanks for the quick reply! Sorry, I should have just said that I cloned the repo yesterday, so should be on the latest pushed commit.

Versions for perl vep.pl:

ensembl : 87.f547798
ensembl-funcgen : 87.0577dd0
ensembl-io : 87.48cb128
ensembl-variation : 87.d12da68
ensembl-vep : 87.27

After running perl -MBio::DB::HTS::Tabix -e'print "OK\n"', I do indeed get OK echo'ed.

Also, running on perl v 5.22.3

from ensembl-vep.

I rechecked the dependencies and it looks like I was missing DBD::mysql. I was previously attempting to run this in --offline mode so I never installed that module.

After installing, it runs now. Perl chose to die at an odd point and with an odd message, but I think I'm good now!

Thanks

from ensembl-vep.

Thanks. Worth knowing as DBD::mysql shouldn't be required given your command line, will have to hunt down where it is being included.

from ensembl-vep.