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Singularity example #2
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Singularity
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Thanks so much! This is a great addition to demonstrate a very useful Snakemake feature. I was able to get it running after making a few minor edits
examples/singularity/README.md
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export SINGULARITY_DOCKER_PASSWORD=Put_Your_GitHub_PAT_Here | ||
snakemake --profile simple/ | ||
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# Confirm the correct time was requested |
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# Confirm the correct time was requested | |
# View the output |
examples/singularity/README.md
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```sh | ||
# set username and password for whatever service you GitHub PAT | ||
export SINGULARITY_DOCKER_USERNAME= | ||
export SINGULARITY_DOCKER_PASSWORD=Put_Your_GitHub_PAT_Here |
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I found this early mention of a GitHub PAT confusing. How about re-ordering the instructions to follow the order of increasing complexity?
- Here's how to run the command (ie just the call to snakemake)
- But if you get this Docker error about a rate limit, then you'll need to authenticate first with your Docker credentials
- And another option for authentication would be to use GitHub
Co-authored-by: John Blischak <jdblischak@gmail.com>
Thanks @CreRecombinase! |
This is is a (relatively) simple example of using singularity with slurm. One thing to note is the addition of the
jobscript
, where I add the slurm-assigned$TMPDIR
to the list of directories mounted in the image. I had some stuff on building a docker image using github actions, but I think that's kind of outside the scope of this repo.