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Add missing required_files to run remotely#1577

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bgruening merged 3 commits intobgruening:masterfrom
nsoranzo:music_deconvolution_required_files
Feb 14, 2025
Merged

Add missing required_files to run remotely#1577
bgruening merged 3 commits intobgruening:masterfrom
nsoranzo:music_deconvolution_required_files

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@nsoranzo
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@nsoranzo nsoranzo commented Feb 14, 2025

Fix the following error when running on a Pulsar destination:

Fatal error: cannot open file '/jetstream2/scratch/main/jobs/65039573/tool_files/scripts/compare.R': No such file or directory

Also:

Fix the following error:

```
Fatal error: cannot open file '/jetstream2/scratch/main/jobs/65039573/tool_files/scripts/compare.R': No such file or directory
```
@bgruening bgruening merged commit 9a01f26 into bgruening:master Feb 14, 2025
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@martenson you had a script to identify those tools, do you? Can you maybe run this over this repo and IUC?

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We should probably also lint this.

@nsoranzo nsoranzo deleted the music_deconvolution_required_files branch February 14, 2025 15:56
anuprulez pushed a commit to anuprulez/galaxytools that referenced this pull request Feb 24, 2025
* Add missing required_files to run remotely

Fix the following error:

```
Fatal error: cannot open file '/jetstream2/scratch/main/jobs/65039573/tool_files/scripts/compare.R': No such file or directory
```

* Replace ubuntu-20.04 runner

https://github.blog/changelog/2025-01-15-github-actions-ubuntu-20-runner-image-brownout-dates-and-other-breaking-changes/

* Lint R scripts
bgruening pushed a commit that referenced this pull request Feb 26, 2025
* update model order

* update main

* add support for png

* update tests

* update tests

* update methods

* add tests

* fix formatting

* Add missing required_files to run remotely (#1577)

* Add missing required_files to run remotely

Fix the following error:

```
Fatal error: cannot open file '/jetstream2/scratch/main/jobs/65039573/tool_files/scripts/compare.R': No such file or directory
```

* Replace ubuntu-20.04 runner

https://github.blog/changelog/2025-01-15-github-actions-ubuntu-20-runner-image-brownout-dates-and-other-breaking-changes/

* Lint R scripts

* remove bioimaging.core

* update tool version

* add input param information

* add end of file line

* update output files

* add image_diff for comparing tiff images in tests

* update tests

* rerun tests

---------

Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
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2 participants