b8b592e17b
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. WWW: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon <bacon4000@gmail.com>
52 lines
1.4 KiB
Text
52 lines
1.4 KiB
Text
--- Makefile.orig 2015-06-23 16:32:51 UTC
|
|
+++ Makefile
|
|
@@ -8,9 +8,13 @@ bindir = $(prefix)/bin
|
|
SEQAN_DIR = SeqAn-1.1
|
|
SEQAN_INC = -I $(SEQAN_DIR)
|
|
INC = $(SEQAN_INC) -I third_party
|
|
-CPP = g++
|
|
-CXX = $(CPP)
|
|
-CC = gcc
|
|
+
|
|
+# Use ?= to allow environment CPP, CC, CXX to take precedence. This avoids
|
|
+# the need to modify the Makefile on different platforms. Package managers
|
|
+# such as FreeBSD ports, MacPorts, etc. set these variables automatically.
|
|
+CPP ?= g++
|
|
+CXX ?= $(CPP)
|
|
+CC ?= gcc
|
|
HEADERS = $(wildcard *.h)
|
|
BOWTIE_MM = 1
|
|
BOWTIE_SHARED_MEM = 1
|
|
@@ -90,10 +94,10 @@ PREFETCH_LOCALITY = 2
|
|
PREF_DEF = -DPREFETCH_LOCALITY=$(PREFETCH_LOCALITY)
|
|
|
|
ifeq (1,$(WITH_TBB))
|
|
- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
|
|
+ LIBS = ${LDFLAGS} $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy
|
|
EXTRA_FLAGS += -DWITH_TBB
|
|
else
|
|
- LIBS = $(PTHREAD_LIB)
|
|
+ LIBS = ${LDFLAGS} $(PTHREAD_LIB)
|
|
endif
|
|
|
|
SEARCH_LIBS =
|
|
@@ -123,7 +127,7 @@ SEARCH_FRAGMENTS = $(wildcard search_*_p
|
|
VERSION = $(shell cat VERSION)
|
|
|
|
BITS=32
|
|
-ifeq (x86_64,$(shell uname -m))
|
|
+ifeq (amd64,$(shell uname -m))
|
|
BITS=64
|
|
endif
|
|
# msys will always be 32 bit so look at the cpu arch instead.
|
|
@@ -143,8 +147,8 @@ ifeq (32,$(BITS))
|
|
$(error bowtie2 compilation requires a 64-bit platform )
|
|
endif
|
|
|
|
-DEBUG_FLAGS = -O0 -g3 -m64
|
|
-RELEASE_FLAGS = -O3 -m64
|
|
+DEBUG_FLAGS = -O0 -g3
|
|
+RELEASE_FLAGS = -O
|
|
NOASSERT_FLAGS = -DNDEBUG
|
|
FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
|
|
|