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Bug 548170 - sci-biology/samtools-1.2: do not install /usr/bin/vcfutils.lua ?
Summary: sci-biology/samtools-1.2: do not install /usr/bin/vcfutils.lua ?
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
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Keywords:
Depends on:
Blocks:
 
Reported: 2015-04-29 18:30 UTC by Martin Mokrejš
Modified: 2017-09-02 12:38 UTC (History)
0 users

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Description Martin Mokrejš 2015-04-29 18:30:14 UTC 
I am not sure but /usr/bin/vcfutils.lua does not seem to be directly executable or we need to DEPEND on luajit?

Maybe we install samtools in a wrong way. Should it be installed as /usr/bin/vcfutils instead?

Somebody please check in this regard all samtools ebuild, including sci overlay.
Comment 1 Martin Mokrejš 2015-04-29 18:33:19 UTC 
Actually, also /usr/bin/r2plot.lua ?
Comment 2 David Seifert gentoo-dev 2016-04-09 19:59:46 UTC 
Removed both lua files in samtools-0.1.20-r2

commit 0f059b5eb7e03f75705f623dc74e27842540da40
Author: David Seifert <soap@gentoo.org>
Date:   Sat Apr 9 21:58:14 2016 +0200

    sci-biology/samtools: Remove lua dep, fix perl shebangs
Comment 3 David Seifert gentoo-dev 2016-04-10 09:22:21 UTC 
Same for samtools-1.3, removed both .lua files

commit 5f3acec053c0f95f355f6c4db5e12994555a4b7a
Author: David Seifert <soap@gentoo.org>
Date:   Sun Apr 10 11:20:56 2016 +0200

    sci-biology/samtools: Remove lua dep, fix perl shebangs
Comment 4 David Seifert gentoo-dev 2017-09-02 12:38:04 UTC 
commit 70386b8c804f2bf2fb7aca4be74d511d765ad1e4
Author:     David Seifert <soap@gentoo.org>
AuthorDate: Sat Sep 2 13:07:41 2017 +0200
Commit:     David Seifert <soap@gentoo.org>
CommitDate: Sat Sep 2 14:37:02 2017 +0200

    sci-biology/samtools: Remove old
    
    Bug: https://bugs.gentoo.org/show_bug.cgi?id=548170
    Bug: https://bugs.gentoo.org/show_bug.cgi?id=620618
    Bug: https://bugs.gentoo.org/show_bug.cgi?id=625504