Comments (1)
The use case is people using rubra from the command line on non cluster environments, or on cluster environments but for tasks not submitted to the queue. The system must have modules in the first place for this feature to make sense, but modules is not commonly found on unix systems.
I propose that we do not implement this feature, instead requires users to manually load modules on the command line before running the pipeline. Clare agrees.
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Related Issues (20)
- Make the pipeline a required argument and remove the --pipeline flag HOT 1
- Modules in the pipeline script's directory can't be imported when it is called via rubra HOT 1
- Add an example pipeline that makes use of the config files
- Putting too many steps out of order results in an error that is not usually seen in Ruffus
- Support SLURM job scheduler HOT 2
- Allow config file to be in different directory to pipeline file
- save a separate shell script for each submitted job
- Generate other image format types for flowchart
- Use shlex.split to parse srun command line
- Make rubra more robust in the face of job errors
- handling of full paths in command line
- example doesn't run out of the box HOT 1
- Trouble install directly from pip HOT 1
- Rubra RedDog error HOT 1
- Make Rubra an installable package in the normal Python way. HOT 1
- Investigate the use of DRMAA to submit jobs to clusters. HOT 2
- Make the installed rubra package executable as a script from the user's path HOT 2
- Add touchfiles as an option alongside print, run, flowchart HOT 2
- The default of rebuild appears to actually be fromstart (which I would expect) ? But docs say it is fromend. HOT 1
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