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ImmPortDB / immport-galaxy

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Are all tools in flowtools available in the Galaxy Toolshed? #6

Open pcm32 opened 4 years ago

pcm32 commented 4 years ago

Hi there!

This is a fantastic set of tools, congrats on the resource. I was wondering if all the tools on this repo inside tools/flowtools are available in the Galaxy Toolshed. I could find some, but not all, but then direct assignment of wrappers in a git repo and repos on a Toolshed is not always straightforward, so I might have missed some.

Would there be any major problems in being able to have all of these tools in the Galaxy toolshed?

This project doesn't seem to be active in terms of commits, is there some other repo where these tools are being maintained (the Galaxy wrappers I mean)? Otherwise, do you intend to maintain any of this?

Thanks!

johnmcampbell13 commented 4 years ago

The ImmPort team is not planning on updating this site and we have no plans at this time to update the tools in the Galaxy toolshed. The person who started this project, moved to another company, approximately 2 years ago, and we are talking about removing this repository. We do continue to use Galaxy and are planning on upgrading to the newest version some time this year if we have the staff and funding. Much of the code needs to be either reviewed or upgraded to work with newer version of R packages and to upgrade the Python code to 3.X. Also the javascript libraries used for the overview pages are pretty old now.

pcm32 commented 4 years ago

Thanks @johnmcampbell13! I would like to suggest some collaboration. Myself and others at AZ are interested in using these tools and contributing to them. My suggestion for doing this would be that we have a repo that only contains the tools plus any scripts that are not provided by the conda packages. That repo could live of course under your organisation, and eventually you could give us write access to it if you don't have the man power to be merging pull requests. In such a repo I could offer to setup CI for testing of the tools and CD for deploying them to the Galaxy Toolshed on any update of the tools. Would this make sense to you? On this new repo you should put everything that you have currently under tools (minus the Galaxy tools that where already there).

Alternatively, you could submit your tools to the galaxy/tool-iuc repo, where we could all interact, although my concern there is that pull request can have very long review periods before merging.

But for setting the CI/CD and making development more versatile, I think it is central to separate the tools git repo from the main Galaxy git repo (which this is a fork of).

Let me know what you think. If you want I can create the repo and then transfer ownership to you.

pcm32 commented 4 years ago

ahh, I see that you have https://github.com/ImmPortDB/immport-galaxy-tools already, so much better!

pcm32 commented 4 years ago

Would you have someone @johnmcampbell13 that could interact with us on this pull request https://github.com/ImmPortDB/immport-galaxy-tools/pull/1 or should we aim to just move work to our own repos and avoiding depending on people related to the original project? Thanks!