search

researchapps / polysolver

Singularity port of HLA typing based on an input exome BAM file and is currently infers infers alleles for the three major MHC class I (HLA-A, -B, -C)
MIT License
13 stars 6 forks source link

Unable to run polysolver docker image #5

Closed zlskidmore closed 6 years ago

zlskidmore commented 6 years ago

Hi,

I've been trying to run polysolver straight from the docker container at https://hub.docker.com/r/sachet/polysolver/ however I keep getting errors specific to parsing the genome assembly parameter. Specifically, regardless of the assembly I supply it always defaults to hg18. I believe this can be traced back to an incompatibility between the shell scripts in /home/polysolver/scripts/ and the underlying shell in the docker container, see stack overflow article below.

https://stackoverflow.com/questions/3265803/bash-string-equality

It's completely possible i'm not understanding something about how docker interacts, if so I appologize, if i'm right however it might be good to replace all the "==" in the shell scripts with "="

vsoch commented 6 years ago

I can't help you here, I don't have any expertise in this area or access to even their Dockerfile or code. This repository was simply a port of the original software into a Singularity image for researchers that needed that to run on a cluster environment.

I can offer to help with your specific questions if you are able to get some original code / Dockerfile to produce the image. From my limited searching this seems to be the paper about it?

https://www.nature.com/articles/nbt.3344

It is irresponsible of the others to not provide support for their tool, but likely they don't know that it's needed. If you want to reach out to them and bring back some resources, I'd be glad to help! :)

zlskidmore commented 6 years ago

Sorry, didn't realize that this repo was a port of the software. I'll go ahead and close this issue, thanks for your time!