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4dn-dcic / tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
MIT License
70 stars 28 forks source link

Transfer ownership of Snakemake tibanna plugin #394

Open johanneskoester opened 1 year ago

johanneskoester commented 1 year ago

As you might have heard, the upcoming Snakemake 8.0 will get support for execution backend plugins (https://github.com/snakemake/snakemake/issues/2409). I have therefore moved the tibanna executor of Snakemake, which was originally developed by @SooLee, into a dedicated plugin: https://github.com/snakemake/snakemake-executor-plugin-tibanna.

The plugin comes with a test framework. Given that you have AWS testing properly set up here, I would love to see the plugin be owned by @4dn-dcic. If you agree, I am happy to transfer the ownership of the plugin from the Snakemake organization to 4dn-dcic. I would be delighted to help with setting up the tests and fix any bugs that I might have introduced with my migration of @SooLee's code into the plugin.

willronchetti commented 1 year ago

Thanks so much for doing this! We would be happy to take ownership of the plugin, and we would welcome contributions in consultation with us to get some tests up for it. If you have ideas for integrated tests we can certainly use our testing account for those. Feel free to request the ownership transfer and I will approve it.

johanneskoester commented 1 year ago

Awesome! So, I tried but it seems permissions don't allow this properly. If you could create public repo here, called snakemake-executor-plugin-tibanna? I will create a PR that adds the source code then.

willronchetti commented 1 year ago

I've gone ahead and created an empty repository under 4dn-dcic here: https://github.com/4dn-dcic/snakemake-executor-plugin-tibanna

Feel free to make the PR!

johanneskoester commented 1 year ago

Seems like it needs one file in it to allow me forking it :-). Can you add an empty README.md?

johanneskoester commented 1 year ago

Wait, much simpler solution! I will make you admin of the original repo, and you transfer the ownership to here. Give me a second.

johanneskoester commented 1 year ago

Done, once you have accepted the invitation, you should be able to transfer the repo, given that you first delete the empty one you just created. Sorry for the hassle.

willronchetti commented 1 year ago

Thanks for doing that, I went ahead and transferred ownership into our org, you can find it at the same link here: https://github.com/4dn-dcic/snakemake-executor-plugin-tibanna

laurentiush commented 3 months ago

Hi, as far as I can see Tibanna does not work with Snakemake 8.0 or later because the plugin is not yet available. Do you have an idea when the executor plugin will become available, so that it is possible to use more recent versions of Snakemake with Tibanna?

scoulondre commented 1 week ago

Hi, as far as I can see Tibanna does not work with Snakemake 8.0 or later because the plugin is not yet available. Do you have an idea when the executor plugin will become available, so that it is possible to use more recent versions of Snakemake with Tibanna?

The most recent combination of snakemake + tibanna that I could set up is snakemake==7.32.4 and tibanna==5.4.3 I am afraid tibanna is dying and I am thinking of migrating to snakemake + kubernetes. Just my 2 cents...

SooLee commented 1 week ago

@Ronchetti, William @.***> Do you need help maintaining the plug-in repo?

On Fri, Oct 18, 2024 at 1:42 PM Stephane Coulondre @.***> wrote:

Hi, as far as I can see Tibanna does not work with Snakemake 8.0 or later because the plugin is not yet available. Do you have an idea when the executor plugin will become available, so that it is possible to use more recent versions of Snakemake with Tibanna?

The most recent combination of snakemake + tibanna that I could set up is snakemake==7.32.4 and tibanna==5.4.3 I am afraid tibanna is dying and I am thinking of migrating to snakemake + kubernetes. Just my 2 cents...

— Reply to this email directly, view it on GitHub https://github.com/4dn-dcic/tibanna/issues/394#issuecomment-2422949403, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHLO3DVF2EES6XFPVK4Q4TZ4FB65AVCNFSM6AAAAABK4NZX46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRSHE2DSNBQGM . You are receiving this because you were mentioned.Message ID: @.***>

willronchetti commented 1 week ago

@SooLee @alexander-veit I am currently transitioning to a new position, so I think this is a question better suited for Alex, but my impression is we are generally very busy with SMaHT and could use the help