igv: import from homebrew/science #18736

iMichka · 2017-09-29T22:01:15Z

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

iMichka · 2017-09-29T22:02:52Z

Companion PR: https://github.com/Homebrew/homebrew-science/pull/6367

ilovezfs · 2017-09-29T22:05:22Z

Formula/igv.rb

Circle and Travis aren't relevant ;)

Woups. Done.

ilovezfs · 2017-09-29T22:09:26Z

Formula/igv.rb

It should be shell_output("#{bin}/igv -b script", 1) if that's the exit code on BrewTestBot. But we need a real test here.

igv has a graphical interface, so not sure how we want to test that.

The -b flag does the follwing (http://software.broadinstitute.org/software/igv/startingIGV):

-b , --batch= Immediately run the supplied batch script after start up.

I think that test is not so bad. We could also try to download a file from a server with it and run a batch script on it. Not sure it is worth it.

yes a -b test would be good

ilovezfs · 2017-10-07T05:58:47Z

2.4.2 is out

iMichka · 2017-10-11T17:10:47Z

Bumping it in science first: https://github.com/Homebrew/homebrew-science/pull/6385

iMichka · 2017-10-11T17:24:20Z

This is now igv 2.4.2, revision 1.

Should I do something for the test or are you happy with it?

iMichka · 2017-10-23T15:10:10Z

@ilovezfs How do you feel about this? You had still some concerns about the test but I am not sure if I can find anything better, see my comment above.

ilovezfs · 2017-10-31T14:33:17Z

Formula/igv.rb

ilovezfs · 2017-10-31T14:33:42Z

Formula/igv.rb

ilovezfs · 2017-10-31T14:33:51Z

Formula/igv.rb

stale · 2017-11-21T15:20:40Z

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

ilovezfs · 2017-11-21T18:59:26Z

🤖, talk to the hand.

iMichka · 2017-11-22T06:01:29Z

Note to myself: 2.4.4 has been pushed to science. I'll try to find some time today to update this PR.

ilovezfs · 2017-11-23T15:36:05Z

ping

iMichka · 2017-11-23T22:48:11Z

igv:
  * C: 14: col 26: Dir(["igv.sh"]) is unnecessary; just use "igv.sh"

I'll change that too.

iMichka · 2017-11-23T22:48:57Z

Actually the line is: libexec.install Dir["igv.sh", "*.jar"]. Seems the audit does not like that?

ilovezfs · 2017-11-24T04:17:02Z

CC @GauthamGoli hmm that doesn't look right to me.

ilovezfs · 2017-11-24T04:18:25Z

@iMichka the audit will probably be happy with

 libexec.install "igv.sh", Dir["*.jar"]

iMichka · 2017-11-24T18:19:55Z

Done.

ilovezfs · 2017-11-25T10:06:53Z

Error Message

failed: brew test igv --verbose

Stacktrace

        Testing igv
/usr/bin/sandbox-exec -f /tmp/homebrew20171124-98985-ovhzc5.sb /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/test.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/igv.rb --verbose
Error: igv: failed
No such file or directory - /usr/local/Cellar/igv/2.4.4_1/libexec/igv

iMichka · 2017-11-28T16:30:50Z

All green :)

ilovezfs · 2017-12-01T16:13:11Z

Formula/igv.rb

This should note the minimum version

iMichka · 2017-12-01T23:12:18Z

Done. The minimum is java 8. No clue if this works with java 9.

sjackman · 2017-12-11T20:16:21Z

How's this PR looking?

iMichka · 2017-12-11T20:18:12Z

Good to go for me.

ilovezfs · 2017-12-12T14:39:30Z

Thanks @iMichka!

iMichka · 2017-12-12T16:26:11Z

Thanks!

ilovezfs reviewed Sep 29, 2017

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iMichka force-pushed the igv branch from 69eb49c to 531ccf6 Compare September 29, 2017 22:07

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ilovezfs added the science Formula was originally in Homebrew/homebrew-science label Sep 30, 2017

iMichka force-pushed the igv branch from 531ccf6 to 4e2abc5 Compare October 11, 2017 17:23

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not needed

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libexec

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no

stale bot added the stale No recent activity label Nov 21, 2017

stale bot removed the stale No recent activity label Nov 21, 2017

iMichka force-pushed the igv branch from 4e2abc5 to 817a4f6 Compare November 22, 2017 20:25

iMichka force-pushed the igv branch from 817a4f6 to 64b0947 Compare November 23, 2017 19:33

iMichka force-pushed the igv branch from 64b0947 to f8ef0c2 Compare November 24, 2017 18:16

GauthamGoli mentioned this pull request Nov 24, 2017

lines_cop: Add condition to prevent false positives Homebrew/brew#3478

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iMichka force-pushed the igv branch from f8ef0c2 to 0b2506f Compare November 24, 2017 19:39

ilovezfs added the test failure CI fails while running the test-do block label Nov 25, 2017

iMichka force-pushed the igv branch from 0b2506f to b0f5037 Compare November 26, 2017 21:34

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This should note the minimum version

ilovezfs removed the test failure CI fails while running the test-do block label Dec 1, 2017

igv: migrate from homebrew-science

d6bddc3

iMichka force-pushed the igv branch from b0f5037 to d6bddc3 Compare December 1, 2017 23:11

GauthamGoli mentioned this pull request Dec 2, 2017

lines_cop: Convert ARGV audit to negative look ahead Homebrew/brew#3518

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ilovezfs changed the title ~~igv: migrate from homebrew-science~~ igv: import from homebrew/science Dec 12, 2017

ilovezfs merged commit 565d754 into Homebrew:master Dec 12, 2017

iMichka deleted the igv branch December 12, 2017 20:55

Homebrew locked and limited conversation to collaborators May 4, 2018

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igv: import from homebrew/science #18736

igv: import from homebrew/science #18736

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