gatk 4.4.0.0 - Githubissues

brewsci / homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

http://brewsci.github.io/homebrew-bio

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gatk 4.4.0.0 #1636

Closed lbergelson closed 1 week ago

lbergelson commented 11 months ago

[x] Have you followed the guidelines for contributing?
[x] Have you checked that there aren't other open pull requests for the same formula update/change?
[x] Have you built your formula locally with brew install --build-from-source FORMULA, where FORMULA is the name of the formula you're submitting?
[x] Does your build pass brew audit --strict FORMULA (after doing brew install FORMULA)?

Update the gatk formula to 4.4.0.0,
set the java dependency to opendjk@17

lbergelson commented 10 months ago

Any thoughts on this? It's failing the bottle build because the bottle build isn't using the right verson of java, although I think I've specified the java version in the dependencies. Am I specifying it wrong or is the bottle build not picking it up correctly?

heuermh commented 10 months ago

Sorry, there is a brew audit failure unrelated to your changes, see https://github.com/brewsci/homebrew-bio/issues/1638

heuermh commented 10 months ago

If you could rebase to pull in fixes made for CI, then we can try to address the jdk 17 issue.

YoshitakaMo commented 10 months ago

The easiest way may be to update your branch once to the latest version and then re-create the pull request again. If anyone knows of a better way to do this, please let me know.

lbergelson commented 10 months ago

Took me a bit to get back to it but I finally rebased it... Looks like one error is solved but I'm still having the java version issue. Is something wrong with my dependency statement maybe?

heuermh commented 9 months ago

In #1647 depends_on is simply openjdk even though it strictly requires JDK 17 or later; this passes CI but I am not sure it would always work on a user's workstation? Or perhaps because at this point and time openjdk is newer than JDK 17 it doesn't matter.

YoshitakaMo commented 1 week ago

I've updated gatk to 4.6.0.0 now. openjdk@17 is used.

heuermh commented 6 days ago

Thank you, @YoshitakaMo!

lbergelson commented 4 days ago

Thanks @YoshitakaMo. I had forgotten about this one.