Consider Publishing Pepr to a Conda repo for Snakemake Integration
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- Dominant language
- R
- Stars
- 3
- Forks
- 1
- PR merge metrics
- No merged PRs in 30d
Description
Hi, big fan of Pepkit, I'm currently using both peppy and pepr. I've come up against a challenge integrating pepr with snakemake. While trying to integrate an R script (that used pepr) into a snakemake pipeline, I can specify the conda environment used to encapsulate this rule. However since it doesn't appear that pepr is published in any conda accessible repos. (AFAICT), when snakemake tries to set up the environment, pepr cannot be installed. I think the solution to this would be adding pepr to bioconda or conda-forge.
Thanks for taking a look at this. Happy to attach/add any info if needed,
Parker
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing how the pepr R package is currently built and the Bioconda or conda-forge submission requirements. Verify that pepr can be installed from the resulting Conda channel within a Snakemake environment. Done means pepr is published in an appropriate Conda repository and can be resolved during environment creation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- build-system, release
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100