Singularity not compatible with GCP life sciences?

[Bob]

Hi everyone,

I am trying to run Snakemake on GCP with google-life-sciences. For containers, I use Singularity which works well with Snakemake on a local cluster.

When I try to run it on GCP, it seems like my container is not recognized, and get a KeyEror: "KeyError: 'FastQC-0.11.9_container.simg'".

I asked my question at the Github of snakemake and just got this response: https://github.com/snakemake/snakemake/issues/457#issuecomment-863296763

Could someone verify that "Singularity containers won't work with Google Life Sciences"?

Thanks in advance!

P.S. My backup plan is using Docker containers but I already have all my Singularity containers ready, so that is why I wanted to be sure.

[Tim Jennison]

Hi Bob,

That is correct. Singularity containers won't work with Life Sciences.

Thanks

Tim

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[Bob]

Hi Tim,

Thank you for verifying this!

Greetings,

Bob