[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-12-g6ecb1b2

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 6ecb1b218db9a353f4d71f9f80f80f0eb3a7ed0e
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sat Mar 10 20:58:14 2012 +0100

    added information about sse_util.h with mising license statement
    patch to disable unknown flags for certain architectures

diff --git a/debian/changelog b/debian/changelog
index 3229b6b..c5bb923 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+bowtie2 (2.0.0-beta5-2) UNRELEASED; urgency=low
+
+  * [Alexandre Mestiasvili]
+  * file sse_util.h has missing copyright header. The Author (Benjamin Langmead) has 
+    confirmed that the file is distributed under GPL3 license.
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Sat, 10 Mar 2012 20:19:53 +0100
+
 bowtie2 (2.0.0-beta5-1) unstable; urgency=low
 
   [ Alexandre Mestiashvili ]
diff --git a/debian/patches/fix_makefile_machine_detection.patch b/debian/patches/fix_makefile_machine_detection.patch
new file mode 100644
index 0000000..4608e98
--- /dev/null
+++ b/debian/patches/fix_makefile_machine_detection.patch
@@ -0,0 +1,49 @@
+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.orig/Makefile
++++ bowtie2/Makefile
+@@ -107,20 +107,36 @@
+ VERSION = $(shell cat VERSION)
+ EXTRA_FLAGS =
+ 
++ARCH := $(shell getconf LONG_BIT)
++UNAME := $(shell uname -m )
+ # Convert BITS=?? to a -m flag
+ BITS=32
+-ifeq (x86_64,$(shell uname -m))
++ifeq (64,$(ARCH))
+ BITS=64
+ endif
+ BITS_FLAG =
+-ifeq (32,$(BITS))
+-BITS_FLAG = -m32
++ifeq ($(UNAME),i386)
++	BITS_FLAG = -m32
+ endif
+-ifeq (64,$(BITS))
+-BITS_FLAG = -m64
++ifeq ($(UNAME),x86_64)
++	BITS_FLAG = -m64
++endif
++ifeq ($(UNAME),'Power Macintosh')
++	ifeq (32,$(BITS))
++		BITS_FLAG = -m32
++	endif
++	ifeq (64,$(BITS))
++		BITS_FLAG = -m64
++	endif
+ endif
+ 
+-SSE_FLAG=-msse2
++SSE_FLAG =
++ifeq ($(UNAME),i386)
++	SSE_FLAG=-msse2
++endif
++ifeq ($(UNAME),x86_64)
++	SSE_FLAG=-msse2
++endif
+ 
+ DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..bc60eae
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix_makefile_machine_detection.patch

-- 
ultrafast memory-efficient short read aligner