conda env activation in template?
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- Dominant language
- R
- Stars
- 184
- Forks
- 53
- Avg merge
- 7d 2h
- Merged PRs (30d)
- 1
Description
Researchers in my lab use conda to manage all bioinformatics software, including python and R packages. We have an available SGE cluster, and to submit jobs to the cluster that require a specific conda environment, we have to include the following the job submission script: source activate MY_CONDA_ENV. Can this line be added to the batchtools SGE template? Can the user specify the particular conda environment via makeClusterFunctionsSGE or submitJob?
Contributor guide
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 reading the SGE template and the makeClusterFunctionsSGE and submitJob entry points named in the issue. Trace how submission scripts are assembled and how a user-supplied conda environment could be represented. Done means an SGE job can activate the requested environment, with coverage for configured and default cases.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- hpc
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100