First off, thanks for your patience.
I’m new to this so learning both how galaxy works as well as
trying to figure out an install for multiple researchers.
The test images I am using are the ones from the usegalaxy.org tutorial.
I loaded them from the urls in that tutorial:
e.g. https://zenodo.org/record/7622545/files/exemplar-002-cycle-01.ome.tiff
On usegalaxy.org, I tried
Upload => Choose from repository => search zenodo
click the Zenodo folder
and a zillion possibilities are there. How would I find them there?
I ended up downloading from the above urls.
On cancer.usegalaxy.org, under libraries, they are in an obvious folder Exemplar_002
On usegalaxy.org:
If I click on Workflows => GTN_Exemplar_002_TMA_workflow_Feb2025
I get a “Workflow Preview” that says last updated Thursday Jul 10 17:10:45 2025 GMT-7 that appears to be when I imported it.
If I click the “Edit” button, I get a dialog that says:
Step 8: Convert dearray images to OME-TIFF
Using version '6.7.0+galaxy3' instead of version '6.7.0+galaxy0' specified in this workflow.
What is the significance of +galaxyN ?
I’ve seen things without any “+galaxy” or “+galaxyN”, as well as the same tool versions (as with basic_illumination here) with different Ns.
Clicking “Continue” puts me in the workflow editor.
How the heck does one get out of the workflow editor without (or with) changing anything?
The only thing that seems to work is the browser back button, which isn’t used anywhere else I’ve found so far.
If I click on step 8: Convert image format,
I see the Galaxy3 version; clicking on the “versions” button shows a Galaxy2 option.
In post #6 you said you loaded the workflow and ran it, and needed to accept one tool update. By “accepting one tool update” do you mean leaving that version at Galaxy3, or changing/accepting something else?
If I click on “step 4: Illumination correction with Basic”, it shows “ImageJ BaSiC shading correction for use with Ashlar (Galaxy Version 1.1.1+Galaxy2)”
Suppose I just want to run the basic_illumination step, not the whole workflow.
If I get out of the editor (browser back button), go to Tools, and search for basic_illumination, it’s not there.
But the workflow didn’t complain about a tool not being installed.
Similarly for ashlar.
If I search for these tools on cancer.usegalaxy.org they show up.
If I load the workflow on usegalaxy.eu
I get a message saying “Imported, but some steps on this workflow have validation errors.” Steps 5, 11, 12 are marked in red with errors:
5. Stitching and registration with Ashlar
rename|markers_file
11. Convert to Anndata
Tool is not installed
12. Scimap phenotyping
Tool is not installed
So on both cancer.usegalaxy.org and usegalaxy.eu, basic_illumination appears to be there and shows up if I search for it in the tools.
I’ve finally figured out it appears to be an issue with the search mechanism on usegalaxy.org:
It appears to be there if I run the whole workflow, as the basic_illumination workflow step completes without errors.
I tried typing “basic”, “BaSiC”, and “illumination” in the search bar and got “No results found”.
If I go to Advanced Tool Search, I see the following behavior:
Filter by name:
BaSic_Illumination no results
basic_illumination no results, even though actual tool name is basic_illumination
basic illumination finds it
basic finds it
illumination finds it
Rather strange behavior that it finds it in the advanced search but not the simple one.
I have some fires to put out so will get back to the galaxy install issue when I have digested a bit more of the admin docs. Thanks again for your patience.