Installing gatk inside singularity container

Question

[lakhujanivijay]

Hi everyone,

I am wondering whether anyone tried installing GATK inside a singularity container. I can see that there is a tutorial on how to install gatk inside a docker container, however, I could not find anything about singularity.

My current approach is to install conda inside my container and then install gatk using conda, however, there are multiple dependency issues with that.

Strange thing is, the same conda environment yml file works locally on my machine however it fails when used in singularity container.

Any ideas?

[GenoMax]

This may be useful: https://learningpatterns.me/posts-output/2018-04-05-gatk-singularity-docker-job-array/

[lakhujanivijay]

Thanks genomax

However I am attempting an installation from the scratch, reason being installing a big set of tools (along with GATK).