I verified that VEP can be run in the terminal successfully. autodie and autodie::Utils are installed in the dir: /local/perl5/lib/perl5/ which is in PERL5LIB. When I try to run hl.vep from python script though its giving an error that Can’t locate autodie/Util.pm in @INC, but the path is there, /local/perl5/lib/perl5/. So, I am not sure whats going wrong here. hail version is 0.2.57.
Are you running on a cluster, or a single node? Is VEP installed on a network-visible file system?
Just in ipython or also with python test_vep.py. Second question - that I am not sure what it means. It can run in terminal, so I should be able to run it from python, I suppose.
Hail uses Apache Spark to orchestrate distributed computing. How is Spark being run? Using default installation on a single computer/server (local mode) or on a cluster (cluster mode)?
also, can you post all the stack traces here?
I guess local mode. We have a folder with installed spark, so I set SPARK_HOME to point to it and add it also to the PATH. I am a bit confused regarding the question since we are not running spark. There is nothing written about spark installation being a prerequisite for hail run:
We just launch ipython, and run several lines of code, thats it. No spark server is running anywhere else.
It was a permissions issue. The @INC path - /local/perl5/lib/perl5/ - needed different folder permissions set up.