galaxyproject / galaxyproject/galaxy

Job resource selector doesn't work with tools from toolshed

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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

Open the contributing 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

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