[148376] trunk/dports/science/bowtie2/files/patch-src-Makefile.diff

[khindenburg at macports.org]

Revision: 148376
          https://trac.macports.org/changeset/148376
Author:   khindenburg at macports.org
Date:     2016-05-06 06:43:12 -0700 (Fri, 06 May 2016)
Log Message:
-----------
bowtie2: add patch

Added Paths:
-----------
    trunk/dports/science/bowtie2/files/patch-src-Makefile.diff

Added: trunk/dports/science/bowtie2/files/patch-src-Makefile.diff
===================================================================
--- trunk/dports/science/bowtie2/files/patch-src-Makefile.diff	                        (rev 0)
+++ trunk/dports/science/bowtie2/files/patch-src-Makefile.diff	2016-05-06 13:43:12 UTC (rev 148376)
@@ -0,0 +1,31 @@
+--- Makefile.orig	2016-04-01 10:04:37.000000000 -0400
++++ Makefile	2016-04-01 10:04:17.000000000 -0400
+@@ -34,26 +34,8 @@
+ BOWTIE_MM = 1
+ BOWTIE_SHARED_MEM = 0
+ 
+-# Detect Cygwin or MinGW
+-WINDOWS = 0
+-MINGW = 0
+-ifneq (,$(findstring MINGW,$(shell uname)))
+-	WINDOWS = 1
+-	MINGW = 1
+-	# POSIX memory-mapped files not currently supported on Windows
+-	BOWTIE_MM = 0
+-	BOWTIE_SHARED_MEM = 0
+-endif
+-
+-MACOS = 0
+-ifneq (,$(findstring Darwin,$(shell uname)))
+-	MACOS = 1
+-	ifneq (,$(findstring 13,$(shell uname -r)))
+-		CPP = clang++
+-		CC = clang
+-		override EXTRA_FLAGS += -stdlib=libstdc++
+-	endif
+-endif
++MACOS = 1
++override EXTRA_FLAGS += -stdlib=libstdc++
+ 
+ POPCNT_CAPABILITY ?= 1
+ ifeq (1, $(POPCNT_CAPABILITY))
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