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frankvogt / vcf2gwas

Python API for comprehensive GWAS analysis using GEMMA
GNU General Public License v3.0
84 stars 29 forks source link

Singularity? #30

Closed Jolleboll closed 6 months ago

Jolleboll commented 1 year ago

Hello!

I was hoping to get this running without root, since Docker is not available on compute clusters. I see there's an older issue about this but it was closed by the submitter before you had a chance to reply.

The sif image created by singularity from your Docker image does not seem to have any executable "vcf2gwas" anywhere in its file tree. There is no fvogt257 folder anywhere, either.

I'm fairly new to containers so don't immediately see how to hack this until it works. Do you have any advice, Frank?

Big thanks in advance!

Joel

nboelte commented 6 months ago

We got a request from one of our HPC users that wanted to install vcf2gwas. We ended up giving them this apptainer recipe, which might also be useful for you.

Bootstrap: docker
From: fvogt257/vcf2gwas

%environment
    source activate python-app

%runscript
    exec vcf2gwas "$@"
Jolleboll commented 6 months ago

Hello and thank you for that! I went with PLINK instead, so don't need this at the moment. But I very much appreciate that you thought of me! :)

Joel