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singularityhub / shpc-registry

A remote registry for Singularity Registry HPC 🖊️
https://singularityhub.github.io/shpc-registry/
Mozilla Public License 2.0
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How to use the Singularity Image after Built from Docker #165

Open kiranpatil222 opened 10 months ago

kiranpatil222 commented 10 months ago

Hi,

I have pulled docker image "docker pull ghcr.io/autamus/gatk:4.2.3.0" and Built SIF image as singularity build gatk_4.2.3.0.sif docker-daemon://ghcr.io/autamus/gatk:4.2.3.0

Now now how do i use for running GATK commands , I need to do same for BWA GATK FASTQC, and VEP

I tried as follows but not working

singularity exec --bind /data gatk_4.2.3.0.sif /opt/view/bin/gatk

vsoch commented 10 months ago

These are container modules intended to be used with singularity-hpc "shpc" https://github.com/singularityhub/singularity-hpc

kiranpatil222 commented 10 months ago

Thanks, you mean these cannot be run on Local Servers with 94 Cores , or is there any alternative way to use it.. Sorry i am new to using singularity docker

kiranpatil222 commented 10 months ago

Thanks i figured it out