snakemake / snakemake/snakemake
Minor: Options `--no-shared-fs` and `--use-conda` are incompatible
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- Dominant language
- Python
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- Forks
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- Avg merge
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- Merged PRs (30d)
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Description
Snakemake version
5.14.0 (bioconda)
Describe the bug
With --no-shared-fs the --use-conda option is simply ignored. Ideally an error message should be displayed or the combination should be made invalid.
Minimal example
Ay Snakefile execution relying on an conda env called with --no-shared-fs --use-conda will fail
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 locating the command-line handling for --no-shared-fs and --use-conda, then reproduce the reported behavior with a Snakefile execution using both options. Determine whether the intended result is an explicit error or rejection of the combination, and verify that the incompatible options no longer proceed silently.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100