rubra
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bjpop
Infrastructure code to support DNA pipeline
Hello, I am running RedDog and I am getting the error that is detailed below. I reported this problem in RedDog GitHub and they suggested that it could be a...
I'm using rubra and would much prefer use actual tagged releases. pip install rubra would be a bonus ;-)
# # example doesn't run out of the box # # Running in examples directory gives missing utils module error rubra example_pipeline.py --config example_config.py --style run [achalk@merri examples]$ ../rubra/rubra.py example_pipeline.py...
Referencing files by their full path results in a file not found error when file exists: rubra/rubra.py /vlsci/VR0244/shared/git/rubra/examples/example_pipeline.py --config /vlsci/VR0244/shared/git/rubra/examples/example_config.py --style run Could not find configuration file: /vlsci/VR0244/shared/git/rubra/examples/example_config.py ls -al...
When a stage crashes and ruffus throws an exception, we end up with the situation where rubra dies but jobs might be launched on the cluster. These jobs probably keep...
At the moment the srun command line is passed to Popen as a string, but it ought to be a list of strings. The recommendation is to use shlex.split to...
Currently we only generate SVGs, but it would be nice to be able to output PNG or JPG.
The current slurmified rubra generates a shell script for each job, but it does not save it with a suitably unique name.