[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-32-g246c7d7

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 246c7d7efaa90790f2ca04880adf2605539fc42c
Merge: de0c32fc6c3d0e92ce98eaafa09ed863df34b488 da842779f3d21d2e844a3ea0bdb10f060787f607
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Jul 17 09:39:57 2012 +0200

    Merge tag 'upstream/2.0.0-beta7'
    
    Upstream version 2.0.0-beta7

diff --combined debian/changelog
index 344b17e,0000000..af0efdf
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,61 -1,0 +1,67 @@@
++bowtie2 (2.0.0-beta7-1) UNRELEASED; urgency=low
++
++  * Imported Upstream version 2.0.0-beta7
++
++ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 17 Jul 2012 09:44:10 +0200
++
 +bowtie2 (2.0.0-beta6-4) UNRELEASED; urgency=low
 +
 +  * debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and 
 +    hurd-i386 SSE is not availbale on others. Closes: #668123 
 +  * debhelper version 9
 +  * debian/rules forced hardening flags
 +  * hardening.patch to inject hardening CPPFLAGS
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Mon, 02 Jul 2012 16:27:10 +0200
 +
 +bowtie2 (2.0.0-beta6-3) unstable; urgency=low
 +
 +  * normalized architecture detection.
 +    For example kfreebsd-amd64 is detected as an amd64 architecture 
 +    and msse flag is set.(Previous commit was wrong) (Closes: #673159)
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Fri, 01 Jun 2012 21:58:49 +0200
 +
 +bowtie2 (2.0.0-beta6-2) unstable; urgency=low
 +
 +  * debian/rules normalized output of dpkg-architecture,  
 +    so for example kfreebsd-amd64 is detected as an amd64 architecture 
 +    and sse flags are enabled for it.
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 31 May 2012 19:22:56 +0200
 +
 +bowtie2 (2.0.0-beta6-1) unstable; urgency=low
 +
 +  * updated debian/watch and get-orig-source to track -source suffix
 +  * Imported Upstream version 2.0.0-beta6
 +  * debian/patches/fix_makefile_machine_detection.patch
 +    use -msse2 only for Intel architectures, Closes: #672526
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Fri, 11 May 2012 08:41:59 +0200
 +
 +bowtie2 (2.0.0-beta5-2) unstable; urgency=low
 +
 +  [ Alexandre Mestiashvili ]
 +  * file sse_util.h has missing copyright header. 
 +    The Author (Benjamin Langmead) has
 +    confirmed that the file is distributed under GPL3 license.
 +
 +  [ Andreas Tille ]
 +  * debian/upstream: Added publication
 +  * debian/patches/fix_makefile_machine_detection.patch + debian/rules:
 +    prevent -mXX and -msse2 switches for non Intel architectures
 +
 +  [ Alexandre Mestiashvili ]
 +  * debian/patches/bowtie2_gcc4.7.patch Closes: #672090
 +  * updated DEP3 headers
 +  * bumperd Standards-Version to 3.9.3
 +  * uname -m doesn't detect 32 bit chroot env - updated patcH
 +
 + -- Andreas Tille <tille at debian.org>  Thu, 26 Apr 2012 13:59:54 +0200
 +
 +bowtie2 (2.0.0-beta5-1) unstable; urgency=low
 +
 +  [ Alexandre Mestiashvili ]
 +  * Initial release (Closes: #660762)
 +
 + -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Wed, 22 Feb 2012 11:03:03 +0100

-- 
ultrafast memory-efficient short read aligner