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Bug 311857 - [science overlay] sci-biology/samtools: new package
Summary: [science overlay] sci-biology/samtools: new package
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High enhancement (vote)
Assignee: Default Assignee for New Packages
URL:
Whiteboard:
Keywords: EBUILD, InOverlay
Depends on:
Blocks: 311847
  Show dependency tree
 
Reported: 2010-03-28 23:51 UTC by Martin Mokrejš
Modified: 2011-02-03 00:21 UTC (History)
2 users (show)

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

Attachments
samtools-0.1.7a.ebuild (samtools-0.1.7a.ebuild,1.03 KB, text/plain)
2010-03-28 23:52 UTC, Martin Mokrejš 		Details
samtools-0.1.7a.ebuild (samtools-0.1.7a.ebuild,1.14 KB, text/plain)
2010-03-29 00:26 UTC, Martin Mokrejš 		Details
samtools-0.1.7a.ebuild (samtools-0.1.7a.ebuild,1.18 KB, text/plain)
2010-08-02 10:14 UTC, Martin Mokrejš 		Details
samtools-0.1.7a.ebuild (samtools-0.1.7a.ebuild,1.19 KB, text/plain)
2010-08-02 13:00 UTC, Martin Mokrejš 		Details
Show Obsolete (2) View All Add an attachment (proposed patch, testcase, etc.)

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Description Martin Mokrejš 2010-03-28 23:51:42 UTC 
This is a set of tools to store and manipulate multiple sequence alignments. Optional for sci-biology/staden package.
Comment 1 Martin Mokrejš 2010-03-28 23:52:04 UTC 
Created attachment 225611 [details]
samtools-0.1.7a.ebuild

Tested ebuild.
Comment 2 Martin Mokrejš 2010-03-29 00:26:09 UTC 
Created attachment 225613 [details]
samtools-0.1.7a.ebuild

staden also needs libbam.a and two headers files.

This ebuild also installs the pre-formated manpage under /usr/man/man1 although I thought it should go under /usr/man/cat1. But, 'man samtools' gives formatted output, probably man(1) is probably smart enough not to touch the formatting anymore?
Comment 3 Martin Mokrejš 2010-08-02 10:14:18 UTC 
Created attachment 241039 [details]
samtools-0.1.7a.ebuild

Added few more header files to src_install() needed by sci-biology/staden to compile. Please note my ebuild differs from the one currently in overlay, which is eapi2 only. I haven't inspected much their differences, sorry.
Comment 4 Martin Mokrejš 2010-08-02 13:00:55 UTC 
Created attachment 241063 [details]
samtools-0.1.7a.ebuild

Added -fPIC flags per discussion with staden developer: https://sourceforge.net/tracker/index.php?func=detail&aid=3038188&group_id=100316&atid=627058

I am quite happy with this ebuild, please move into official portage tree.
Comment 5 Martin Mokrejš 2010-11-25 23:29:19 UTC 
It seems I managed to commit my first ebuild (samtools-0.1.7a.ebuild) to the overlay, please test, report and eventually cherry-pick into the official tree and close this bug if it is ok.
Comment 6 Andrey Kislyuk (RETIRED) gentoo-dev 2011-02-03 00:21:56 UTC 
In main tree and request filed for stable, congrats Martin