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immediately after commenting on this PR.

Clicking on the notification redirects me to this action. As far as I see, some action was supposed to be triggered by my comment, but did not. Is there something misconfigured and might this be related to the failing PR?

The rfove tool fails to run on Galaxy EU:

/data/jwd02f/main/064/693/64693286/tool_script.sh: line 9: /rfove: No such file or directory

History: https://usegalaxy.eu/u/e26918e6b1264c81874871c01e988195/h/rfove-test

But both, testing locally with planemo test --docker and in CI works:

• https://github.com/BMCV/galaxy-image-analysis/actions/runs/6856997686
• https://github.com/BMCV/galaxy-image-analysis/actions/runs/6847881219
• https://github.com/BMCV/galaxy-image-analysis/actions/runs/6857223204
• https://github.com/BMCV/galaxy-image-analysis/actions/runs/6847980920

Sources: https://github.com/BMCV/galaxy-image-analysis/blob/master/tools/rfove/rfove.xml#L19

Might there be an issue with the Docker container? I'm not very experienced with Docker containers in Galaxy:

    <requirements> 
        <container type="docker">docker.io/kostrykin/rfove:@TOOL_VERSION@</container>
    </requirements>

Dockerfile: https://github.com/kostrykin/rfove/blob/master/Dockerfile

xref #89 #91 usegalaxy-eu/usegalaxy-eu-tools#645

• one screenshot of paraview in Galaxy

Would be cool to have a tool to execute "arbitrary" ImageJ macros (https://imagej.net/ij/developer/macro/macros.html). For security reasons it should be the normal macros (not via python / java script).

Could be simply one image in and one image out.

Or more complicated ones where users set parameters in the tool form (maybe like here).

Hello @bgruening , thanks for merging the PR of adding two new tools. However, the tool landmark_registration_ls is not accessible at usegalaxy.eu, while the other one works perfectly.

Maybe the reason is that it uses the same tool name as the tool landmark_registration (despite of unique tool IDs)?

When running the recent tool versions updated by #65 and #66, an error occurs:

python: can't open file '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/imgteam/superdsm/700ae37e5c69/superdsm/run-superdsm.py': [Errno 2] No such file or directory

and

python: can't open file '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/5bf8eb50b280/count_objects/count_objects.py': [Errno 2] No such file or directory

respectively. Maybe the web handlers are out of sync again? @bgruening

Here is a link to the errors: https://usegalaxy.eu/u/e26918e6b1264c81874871c01e988195/h/unnamed-history-1

Hi @bgruening , thanks for merging the updates of the tool "points_association_nn". I have seen that this tool has been updated to version 0.02 in the Galaxy tool shed, but it is still 0.01 on usegalaxy.eu.

Will tool updates on usegalaxy.eu be executed also on Saturdays like adding new tools? If so, is it possible to have this tool updated on usegalaxy.eu sooner? Waiting until the weekend seems slightly too long to us as we would like to include this tool and a related workflow in our new paper to be submitted within this week.

Thanks!

I was experiencing some inconsistent behavior when using planemo test for a tool I am developing. In search for the cause I had to remove ~/miniconda3 on my system, which was then re-created by the next invocation of planemo test.

When running planemo test now, for example, for the tool segmetrics, the following output is obtained and repeated a few times with some variations regarding the parameters passed to conda create:

galaxy.tool_util.deps.conda_util DEBUG 2023-06-19 16:13:33,607 [pN:main.1,p:1021725,tN:LocalRunner.work_thread-0] Executing command: ~/miniconda3/bin/conda create -y --quiet --strict-channel-priority --experimental-solver libmamba --override-
channels --channel conda-forge --channel bioconda --channel defaults --name mulled-v1-138080b4d40419e12a6a019e79f27ae713ae4ee1e04039908a3b046c06674243 segmetrics=1.4 pandas=0.23.4
galaxy.tool_util.deps.conda_util DEBUG 2023-06-19 16:13:33,880 [pN:main.1,p:1021725,tN:LocalRunner.work_thread-0] Executing command: ~/miniconda3/bin/conda create -y --quiet --experimental-solver libmamba --override-channels --channel conda-f
orge --channel bioconda --channel defaults --name mulled-v1-138080b4d40419e12a6a019e79f27ae713ae4ee1e04039908a3b046c06674243 segmetrics=1.4 pandas=0.23.4
galaxy.tool_util.deps.resolvers.conda DEBUG 2023-06-19 16:13:34,152 [pN:main.1,p:1021725,tN:LocalRunner.work_thread-0] Removing failed conda install of [CondaTarget[segmetrics,version=1.4], CondaTarget[pandas,version=0.23.4]]
galaxy.tool_util.deps.conda_util DEBUG 2023-06-19 16:13:34,152 [pN:main.1,p:1021725,tN:LocalRunner.work_thread-0] Executing command: ~/miniconda3/bin/conda create -y --quiet --strict-channel-priority --experimental-solver libmamba --override-
channels --channel conda-forge --channel bioconda --channel defaults --name [email protected] segmetrics=1.4

The creation of the environment ultimately fails.

Manually repeating the command reported above yields the error causing the failure:

~/miniconda3/bin/conda create --strict-channel-priority --experimental-solver libmamba --override-channels --channel conda-forge --channel bioconda --channel defaults --name test pandas

usage: conda create [-h] [--clone ENV] (-n ENVIRONMENT | -p PATH) [-c CHANNEL] [--use-local] [--override-channels] [--repodata-fn REPODATA_FNS] [--experimental {jlap,lock}] [--strict-channel-priority] [--no-channel-priority]
                    [--no-deps | --only-deps] [--no-pin] [--copy] [-C] [-k] [--offline] [-d] [--json] [-q] [-v] [-y] [--download-only] [--show-channel-urls] [--file FILE] [--no-default-packages] [--solver {classic} | --experimental-solver {classic}]
                    [--dev]
                    [package_spec ...]
conda create: error: argument --experimental-solver: invalid choice: 'libmamba' (choose from 'classic')

Without the --experimental-solver libmamba flag, the above command works. Can planemo test somehow be told not to use this flag? Removing ~/.planemo on my system to make sure it is reset to a clean state does not make a change.

Note that this isn't related to any particular tool. Besides of segmetrics, I also tried planemo test for the tools 2d_auto_threshold, 2d_feature_extraction, and overlay_images, which all yield the behavior described above.

Is this maybe related to galaxyproject/galaxy#16124?

I made a list of potential tools which could be implemented for image processing and analysis. The list is derived from a comparison of the tools present in Galaxy with some workflow developed by the KNIME Image Processing Extension. Overall, there is a good presence of tools and it possible to reproduce most of the workflow with few modifications.

https://galaxyproject.org/news/2024-03-08-hackathon-imaging/#workflow-translation-from-knime-to-galaxy

Binary

• Fill Holes (Fill black holes in binary images)
  Skimage -> binary_fill_holes
  Morphological Image Operations
• Perform morphological operations (like erode and dilate or open and close) on images. As far as I saw, it is not possible to perform these single operations in Galaxy
  - Erode: Shrink bright areas.
  - Dilate: Grow bright areas.
  - Open: Erode followed by Dilate. Erases tiny bright spots.
  - Close: Dilate followed by Erode. Erases tiny dark holes.
  Example: https://imagej.net/ij/plugins/gray-morphology.html
  In General: https://github.com/ijpb/MorphoLibJ/

Process

• Iverter -> Inverts Images
  Example: https://imagej.net/ij/plugins/inverter.html
• OrientationJ Measurement -> This node performs quantitative orientation measurements according to the ImageJ plugin OrientationJ
  Example: https://github.com/Biomedical-Imaging-Group/OrientationJ #110

Labelling

• Voronoi Segmentation - Performs a Voronoi based segmentation of images. Requires an input table with a source image and a labeling of the corresponding seed regions.
  Examples: https://bioimagebook.github.io/chapters/2-processing/6-transforms/imagej.html

Quantification

• Extract features from the Voronoi based segmentation

Visualization

• Overlay the colorized labeled map on the original image by keeping the same color palette

currently, when I use overlay_images to overlay an image with a segmentation mask, the output is tiff. This means I cannot view the result in the browser without converting it to png first.

since overlays of masks and images are only used for visualization, it would make sense to output png instead of tiff by default

The following tools / tool versions should be marked as hidden and deprecated:

• All revisions of 2d_split_binaryimage_by_watershed,
  see usegalaxy-eu/usegalaxy-eu-tools#647
• Revision 7989264b5780 of segmetrics, corresponding to the tool version 1.4.0-1,
  see #88
• Revisions 4b6c2135e547 and b32f5368e279 of bioformats2raw due to the bug described in #102
• Revision 7db4fc31dbee of ip_threshold, corresponding to the tool version 0.18.1+galaxy0, see #112
• The tool 2d_local_threshold is already marked as deprecated, but not hidden.
• The curl_post tool should be marked deprecated.