Singularity example #2
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Singularity
jdblischak
requested changes
Aug 5, 2021
examples/singularity/README.md
Outdated
| export SINGULARITY_DOCKER_PASSWORD=Put_Your_GitHub_PAT_Here | ||
| snakemake --profile simple/ | ||
|
|
||
| # Confirm the correct time was requested |
There was a problem hiding this comment.
Suggested change
| # Confirm the correct time was requested | |
| # View the output |
examples/singularity/README.md
Outdated
| ```sh | ||
| # set username and password for whatever service you GitHub PAT | ||
| export SINGULARITY_DOCKER_USERNAME= | ||
| export SINGULARITY_DOCKER_PASSWORD=Put_Your_GitHub_PAT_Here |
There was a problem hiding this comment.
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>
jdblischak
approved these changes
Aug 5, 2021
|
Thanks @CreRecombinase! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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$TMPDIRto 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.