snakemake / snakemake/snakemake
Permission issue when caching directories
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- Dominant language
- Python
- Stars
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- Avg merge
- 4d 12h
- Merged PRs (30d)
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Description
It looks like snakemake 5.13.0 has issues caching whole directories.
When performing a rule whose output-directory is to be cached snakemake fails.
It shows that the output directory actually got moved to the cache-directory but it is not possible to access it. This is due to a missing execution permission.
Adding the missing permission manually allows the workflow to move on.
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
Reproduce the issue with Snakemake 5.13.0 using a rule whose output is a cached directory, then inspect the directory after it is moved into the cache. Confirm that the cached output remains accessible without manually adding execute permission.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100