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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
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Adding GPU parameters for instaGRAAL #1317

Closed gulsumgudukbay closed 11 months ago

gulsumgudukbay commented 1 year ago

Added GPU parameters for instaGRAAL to allow execution of the GPU-supported version of instaGRAAL.

bgruening commented 1 year ago

Thanks @gulsumgudukbay! Since which Galaxy version is this supported? I guess we would need to add a profile version? Or we simply assume that older Galaxy will ignore it?

bgruening commented 1 year ago

ping @sanjaysrikakulam

gulsumgudukbay commented 1 year ago

Thanks @gulsumgudukbay! Since which Galaxy version is this supported? I guess we would need to add a profile version? Or we simply assume that older Galaxy will ignore it?

It is supported after 23.0 (since the packages were released in that version). Could you please elaborate on the profile version? is it a specification for the Galaxy version for the requirements?

bgruening commented 1 year ago

See here: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-profile

gulsumgudukbay commented 1 year ago

See here: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-profile

I added the profile tag

gulsumgudukbay commented 1 year ago

See here: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-profile

Do I have to do anything else for the tests?

gulsumgudukbay commented 1 year ago

I think the profile version gave an error. I fixed it.

gulsumgudukbay commented 1 year ago

See here: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-profile

Is 23.0.1 not a valid profile?

bgruening commented 1 year ago

Not yet, 23.1 is not yet released officially. Sorry.

gulsumgudukbay commented 12 months ago

Not yet, 23.1 is not yet released officially. Sorry.

I also tried 23.0 (commit ID [6ba97a4]), however, that also gave an error (Lint tool-list test). I see that 23.0 is in the link you provided. Could you please let me know why it throws an error and how I can solve the issue?

mvdbeek commented 12 months ago

Or we simply assume that older Galaxy will ignore it?

That's not an assumption, I would add your regular profile version (was it one year from the last stable release ?). The linting is unrelated to those changes here.

gulsumgudukbay commented 11 months ago

Or we simply assume that older Galaxy will ignore it?

That's not an assumption, I would add your regular profile version (was it one year from the last stable release ?). The linting is unrelated to those changes here.

So 23.0 profile version should be correct?

mvdbeek commented 11 months ago

You don't technically need 23.0. I'd make it 22.01 if you want to follow https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-profile

gulsumgudukbay commented 11 months ago

You don't technically need 23.0. I'd make it 22.01 if you want to follow https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-profile

But the GPU tags are released in the 23.0 Galaxy version. If I make the profile 22.01, will it comply with the 23.0 Galaxy version changes? (I thought the profile and Galaxy version are related)

mvdbeek commented 11 months ago

But the GPU tags are released in the 23.0 Galaxy version.

So they'll be ignored, that's ok.

gulsumgudukbay commented 11 months ago

But the GPU tags are released in the 23.0 Galaxy version.

So they'll be ignored, that's ok.

I updated the profile.

gulsumgudukbay commented 11 months ago

See here: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-profile

Hi Bjorn, could you please re-trigger the tests if everything looks fine (also for the racon PR)?

gulsumgudukbay commented 11 months ago

The linting fails because there are two parameters with the same name ("bomb" parameter). Since it is unrelated to the GPU tags, I am not sure how to proceed. @bgruening @mvdbeek

bgruening commented 11 months ago

Thanks @gulsumgudukbay !