[med-svn] r13382 - trunk/packages/bowtie/trunk/debian/patches

[Ognyan Kulev]

Author: ogi
Date: 2013-04-23 13:36:06 +0000 (Tue, 23 Apr 2013)
New Revision: 13382

Added:
   trunk/packages/bowtie/trunk/debian/patches/machine_bits_detection.patch
Modified:
   trunk/packages/bowtie/trunk/debian/patches/series
Log:
Added machine_bits_detection.patch.


Added: trunk/packages/bowtie/trunk/debian/patches/machine_bits_detection.patch
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/machine_bits_detection.patch	                        (rev 0)
+++ trunk/packages/bowtie/trunk/debian/patches/machine_bits_detection.patch	2013-04-23 13:36:06 UTC (rev 13382)
@@ -0,0 +1,35 @@
+Description: Properly detect 32/64-bit machine architecture
+Author: Ognyan Kulev <ogi at tower.3.bg>
+Applied-Upstream: no
+Last-Update: 2013-04-23
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bowtie-1.0.0.orig/Makefile
++++ bowtie-1.0.0/Makefile
+@@ -93,23 +93,9 @@
+ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
+ VERSION = $(shell cat VERSION)
+ 
+-BITS=32
+-# cygwin will stay 32 bit for now.
+-ifeq (1,$(MINGW))
+-    # msys will always be 32 bit so look at the cpu arch.
+-    ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITEW6432)))
+-        BITS=64
+-    else
+-        ifneq (,$(findstring AMD64,$(PROCESSOR_ARCHITECTURE)))
+-            BITS=64
+-        endif
+-    endif
+-endif
+-
+-ifeq (1,$(LINUX))
+-    ifeq (x86_64, $(shell uname -p))
+-        BITS=64
+-    endif
++BITS = 32
++ifeq (64,$(shell getconf LONG_BIT))
++    BITS = 64
+ endif
+ 
+ # Convert BITS=?? to a -m flag

Modified: trunk/packages/bowtie/trunk/debian/patches/series
===================================================================
--- trunk/packages/bowtie/trunk/debian/patches/series	2013-04-22 19:58:32 UTC (rev 13381)
+++ trunk/packages/bowtie/trunk/debian/patches/series	2013-04-23 13:36:06 UTC (rev 13382)
@@ -3,3 +3,4 @@
 seqan-fix-setBegin-call.patch
 seqan-rename-ChunkPool.patch
 seqan-rename-fill-to-resize.patch
+machine_bits_detection.patch