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Bug 524252 - sci-biology/cufflinks-2.2.1 should not depend on <sci-biology/samtools-1.0
Summary: sci-biology/cufflinks-2.2.1 should not depend on <sci-biology/samtools-1.0
Status: RESOLVED FIXED
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:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2014-10-01 20:32 UTC by Michael Schubert
Modified: 2014-10-02 08:01 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
cufflinks-2.2.1 ebuild for samtools-1.0 (cufflinks-2.2.1.ebuild,1014 bytes, text/plain)
2014-10-01 20:32 UTC, Michael Schubert
Details

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Description Michael Schubert 2014-10-01 20:32:10 UTC
Created attachment 385922 [details]
cufflinks-2.2.1 ebuild for samtools-1.0

When using -lhts for BAM library, cufflinks-2.2.1 works perfectly fine with samtools-1.0

See attached ebuild for an example (at src_compile, ignore src_configure, that's what I came up with without known the CFLAGS patch).
Comment 1 Jeroen Roovers (RETIRED) gentoo-dev 2014-10-01 23:38:55 UTC
  25 Sep 2014; Justin Lecher <jlec@gentoo.org> cufflinks-1.3.0-r1.ebuild:
  Fix dep due to uncompatible samtools release

This kind of crappy solutions happen a lot?
Comment 2 Justin Lecher (RETIRED) gentoo-dev 2014-10-02 08:01:21 UTC
+*cufflinks-2.2.1-r1 (02 Oct 2014)
+
+  02 Oct 2014; Justin Lecher <jlec@gentoo.org> +cufflinks-2.2.1-r1.ebuild,
+  +files/cufflinks-2.2.1-flags.patch, +files/cufflinks-2.2.1-hts.patch:
+  Drop debugging flags, fix compatibility with newer samtools, #524252
+