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Bug 572054 - sci-biology/tophat-2.1.0 version bump
Summary: sci-biology/tophat-2.1.0 version bump
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal enhancement (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2016-01-16 03:36 UTC by Shunran
Modified: 2016-04-09 18:59 UTC (History)
0 users

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Description Shunran 2016-01-16 03:36:39 UTC 
Request for version bump to 2.1.0 in order to work with sci-biology/bowtie-2.2.6. The current version is already a few years old and can no longer function.

Also Project URL changed to https://ccb.jhu.edu/software/tophat

Build hint: parallel make seems to be broken with this package (tested with make -j20 with no luck), but make -j1 works. 

Need a patch to remove SeqAn shipped with the source code, and modify the configure.ac line 108 in order to use the sci-biology/seqan-1.3.

Depend on bowtie and sci-biology/seqan-1.3
Comment 1 David Seifert gentoo-dev 2016-01-19 18:19:15 UTC 
We are well aware that tophat in the tree is pretty broken. We'll rework this hopefully soon, but it requires some reengineering efforts, SLOTting samtools, seqan etc.
Comment 2 David Seifert gentoo-dev 2016-04-09 18:59:03 UTC 
SeqAn and samtools unbundled, updated to latest 2.1.1
Depends on samtools:0.1-legacy now, which does not block SLOT=0 anymore.

commit 3bae7944956edffc244eb7d8e55bc0c786013ed0
Author: David Seifert <soap@gentoo.org>
Date:   Sat Apr 9 20:37:04 2016 +0200

    sci-biology/tophat: Version bump, use samtools:0.1-legacy
    
    Gentoo-Bug: 545154, 546816, 566494, 572054
    * EAPI=6
    * Unbundle samtools and SeqAn
    * Fix broken shebangs in python scripts