I noticed workflow versions (v1,v2…) in workflowhub and myexperiments but it’s not available to the galaxy shared workflow.
Is it possible to get all versions of a particular workflow??
1 Like
Hi @khairul0026
Yes, Galaxy now keeps track of workflow versioning. The Galaxy workflow version is part of each workflow’s metadata. To view the version in Galaxy, open the workflow in the editor, and the current version will be listed in the far right panel. Navigate the available versions using the pull-down menu.
Note that a workflow publication site may have its own versioning system. You can keep track of both and anything else important to you within your copy of the workflow – details below.
It depends on what the original authors published and how the workflow hosting system versions published content uploaded to the site. Example: This workflow has two published versions that can be navigated/downloaded sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLICON-IVAR-PANGOLIN-NEXTCLADE
Technically, if the workflow was published in the last year or so, it will include at least one Galaxy version available in the workflow’s metadata. The author may also have annotated the workflow with other details. Examples: source repository, citation information, related publications, or public data sources.
Workflow versioning within the workflow itself may not be included in workflows created/published before the functionality was added to Galaxy. This means that when you import a workflow without built-in versioning, the default version will be set by Galaxy. Any changes you make from that point forward will be tracked and incorporated.
You can also add more annotation to your copy of the workflow in the description. This could capture information about the source (URL, 3rd party version, dates published/obtained, authors/citations) or anything else informative that you want to track.
Recent Galaxy release highlights about workflows:
- September 2020 Galaxy Release (v 20.09) — Galaxy Project 23.1.1.dev0 documentation
- January 2021 Galaxy Release (v 21.01) — Galaxy Project 23.1.1.dev0 documentation
Workflow authors and developers:
- Workflows published by the wider Galaxy community (some are members of the two groups below) can be found here Workflows and here myExperiment - Workflows. Both sites have instructions and several use-cases are covered in the tutorials below. Help is also included in Galaxy on the “Workflows > Import” form.
- Workflows published by the IWC (“Intergalactic Workflow Commission”) are authored by this group GitHub - galaxyproject/iwc: Galaxy Workflows maintained by the Intergalactic Workflow Commission and are also published here Dockstore
- Workflows published by the GTN (“Galaxy Training Network”) are authored by this group GitHub - galaxyproject/training-material: A collection of Galaxy-related training material and are primarily published here https://training.galaxyproject.org with one here (so far) Dockstore
If a workflow is published at a public site or included in a publication, import it to the Galaxy server where you are working to use it. You may need to modify a workflow – open it in the editor and review any messages about updated tool versions or similar. If you are working at your own Galaxy server, you may need to install or update tools and reference data. Some workflow authors may also publish a pre-configured Docker Galaxy. One example is the GTN – find any associated docker images on the topic category pages in the section “Galaxy instances” and/or included in the “Available on these Galaxies” pull-down menu included directly on tutorial pages.
GTN Tutorials about workflows:
Hope that helps!
1 Like
@khairul0026 Galaxy’s internal workflow versioning and the external one you’re seeing in the workflowhub, for example, are not the same thing. To get different workflowhub versions (we like to call them releases in the Galaxy world to distinguish them from Galaxy’s internal versions), you will need to import them as separate workflows into Galaxy.
2 Likes
While I published a workflow in galaxy repository, it’s always becoming a new workflow instead of versioning, but in my workflow list it’s like a different versions like v1, v2… I am hoping to get this type of versioning (v1,v2…) if I share same workflow in the galaxy repository
Is it possible to share workflow using different versions in galaxy repositories? For me it’s becoming new workflow instead of versioning
@khairul0026 are you talking about publishing a workflow on a Galaxy instance so that others can find it under “Shared Data” → “Workflows”?
If so, then the answer is: when people are importing a Galaxy-published workflow into their own account they will import only the specific state the workflow is in at that moment. Importing is a copy operation so afterwards the other user owns the copy and can start modifying, which will create new versions of their workflow.
If you modify the original workflow later, this will be reflected directly in the published workflow in Shared Data, but will not affect the other user’s copy. If they want to get your latest changes, they will need to re-import the published workflow, i.e. create another copy.
The best way to deal with public-facing workflow versions is to export your workflow file and deposit it in a public version-control system. Dockstore and workflowhub are repositories tailored specifically to scientific workflows, but you can use, for example, a github repo to host your workflow and people can use Galaxy’s workflow import functionality to get the workflow directly from there. This way everyone’s aware of your versions and can refer to them properly.
1 Like