search

cpwardell / FiNGS

Filters for Next Generation Sequencing
Apache License 2.0
10 stars 0 forks source link

Trying to run fings in Cromwell. #3

Closed njbernstein closed 3 years ago

njbernstein commented 3 years ago

Hi there,

I'm trying Fings out in a cromwell pipeline.

The container seems to get built fine, but the fings command fails for the following reason.

[UserAction] Unexpected exit status 2 while running "/bin/bash /cromwell_root/script": python: can't open file '/opt/conda/lib/python3.7/site-packages/fings/FiNGS.py': [Errno 2] No such file or directory

The command I run in the container is 

fings -t test.bam -v test-filtered.vcf

Any thoughts?

njbernstein commented 3 years ago

Looks like the entrypoint for the docket container is wrong. '/opt/conda/lib/python3.7/site-packages/fings/FiNGS.py' doesnt run even when I build it from scratch

njbernstein commented 3 years ago

The path now needs to be: /opt/conda/lib/python3.8/site-packages/fings/FiNGS.py

njbernstein commented 3 years ago

You should have the FiNGS.py be able to be accessed just with fings command by using entrypoints in your setup.py. That way you'll avoid hardcoding a path like above.

cpwardell commented 3 years ago

Thanks for the tip; I added a fings command to the entrypoint.