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Singularity example #2

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merged 8 commits into from
Aug 5, 2021
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CreRecombinase
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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.

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@jdblischak jdblischak left a comment

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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

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export SINGULARITY_DOCKER_PASSWORD=Put_Your_GitHub_PAT_Here
snakemake --profile simple/

# Confirm the correct time was requested
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Suggested change
# Confirm the correct time was requested
# View the output

```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

CreRecombinase and others added 2 commits August 5, 2021 11:12
Co-authored-by: John Blischak <jdblischak@gmail.com>
@jdblischak jdblischak merged commit 789071a into jdblischak:main Aug 5, 2021
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Thanks @CreRecombinase!

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2 participants