galaxyproject / galaxyproject/galaxy
Job resource selector doesn't work with tools from toolshed
- Dominant language
- Python
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Description
It seems that we cannot add a job resource selector to tools installed from toolshed. I see two reasons:
- in the [source code](https://github.com/galaxyproject/galaxy/blob/release_20.01/lib/galaxy/tools/__init__.py#L1253), the tool wrapper id is compared to the tool id find in the job_conf.xml. They are different, in the job_conf.xml it looks like _toolshed.g2.bx.psu.edu/repos/userid/category/toolid/toolversion_
- the tool id from job_conf.xml is switched to lower case at some point before being compared to the tool wrapper id while the comparison is case sensitive
I can try to write a patch but I'm not sure where to start.
Can somebody tell me why the shedtool id we write in the job_conf.xml is not the wrapper tool id?
Thanks
Contributor guide
Research direction
Start at lib/galaxy/tools/__init__.py around line 1253 and trace how the tool wrapper ID is compared with the ID from job_conf.xml. Inspect the Toolshed ID format and the point where the job configuration ID is lowercased. Done means job resource selectors can match Toolshed-installed tools without incorrect case-sensitive or format-dependent comparisons.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100