frattalab / frattalab/PAPA

sge profile not working for UCL SGE cluster

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bug
Dominant language
Python
Stars
2
Forks
0
PR merge metrics
No merged PRs in 30d

Description

I think because the profile lacks some default options that UCL SGE cluster requires, and also tries to set a tmpdir which UCL CS cluster forbids.

Need to experiment/make custom profile for UCL CS SGE cluster.

Contributor guide

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Research direction

Inspect the repository's existing SGE profile and compare its default options and tmpdir behavior with the UCL CS SGE requirements described here. Confirm the required options and forbidden tmpdir setting with a test run on that cluster; done when the profile runs the pipeline there without those configuration errors.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, hpc
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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