Question: Installing gatk inside singularity container
1
gravatar for lakhujanivijay
4 months ago by
lakhujanivijay5.2k
India
lakhujanivijay5.2k wrote:

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?

container singularity gatk • 229 views
ADD COMMENTlink written 4 months ago by lakhujanivijay5.2k

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

ADD REPLYlink written 4 months ago by genomax90k

Thanks genomax

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

ADD REPLYlink written 4 months ago by lakhujanivijay5.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1914 users visited in the last hour