[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-18-g2f459ff

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 63de8d6638c5c54675387b2e96a46b8351436639
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed May 9 14:07:27 2012 +0200

    uname -m doesn't detect 32 bit chroot env

diff --git a/debian/patches/fix_makefile_machine_detection.patch b/debian/patches/fix_makefile_machine_detection.patch
index 7487d48..050ba38 100644
--- a/debian/patches/fix_makefile_machine_detection.patch
+++ b/debian/patches/fix_makefile_machine_detection.patch
@@ -2,9 +2,9 @@ Subject: Attemp to adapt build flags to built package on all supported
  architectures.
 Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Date: 2012-03-10
---- bowtie2-2.0.0-beta5.orig/Makefile
-+++ bowtie2-2.0.0-beta5/Makefile
-@@ -107,20 +107,38 @@
+--- bowtie2.orig/Makefile
++++ bowtie2/Makefile
+@@ -107,20 +107,33 @@
  VERSION = $(shell cat VERSION)
  EXTRA_FLAGS =
  
@@ -25,14 +25,9 @@ Date: 2012-03-10
 + UNAME := $(shell uname -m )
 + # Convert BITS=?? to a -m flag
 + BITS=32
++ BITS_FLAG = -m32
 + ifeq (64,$(ARCH))
-+ BITS=64
-+ endif
-+ BITS_FLAG =
-+ ifeq ($(UNAME),i386)
-+	BITS_FLAG = -m32
-+ endif
-+ ifeq ($(UNAME),x86_64)
++	BITS=64
 +	BITS_FLAG = -m64
 + endif
 + ifeq ($(UNAME),'Power Macintosh')

-- 
ultrafast memory-efficient short read aligner