Bug 548170

Summary:	sci-biology/samtools-1.2: do not install /usr/bin/vcfutils.lua ?
Product:	Gentoo Linux	Reporter:	Martin Mokrejš <mmokrejs>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED OBSOLETE
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

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