The following commit has been merged in the master branch:
commit 6ecb1b218db9a353f4d71f9f80f80f0eb3a7ed0e
Author: Alexandre Mestiashvili <[email protected]>
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 <[email protected]> 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
<[email protected]>
+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
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