galaxyproject / galaxyproject/usegalaxy-tools

Config problem abims_xcms_retcor 3.12.0+galaxy0

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bug
Dominant language
Shell
Stars
22
Forks
70
Avg merge
1d 3h
Merged PRs (30d)
25

Description

tool_id=toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0
update this also presents with the same error tool_id=toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0

stderr

Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: source_local -> source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file '/jetstream2/scratch/main/jobs/56303532/tool_files/lib.r': No such file or directory
Execution halted

Test history https://usegalaxy.org/u/jen-galaxyproject/h/test-lcms-preprocessing

Work-around for end users

When running your own analysis, or GTN tutorials such as https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html, that include this tool, consider working at UseGalaxy.fr instead until this ticket closes out.
Note: workflow4metabolomics.usegalaxy.fr is a subdomain of the same usegalaxy.fr french server. You can work at either and your account at both is the same.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the linked test history and the two affected tool IDs, abims_xcms_retcor and abims_xcms_fillPeaks. Trace how each tool packages or locates tool_files/lib.r and reproduce the missing-file error. Done means both tools run without the reported connection error on the affected server.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
data, tooling
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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