diff options
Diffstat (limited to 'biology/bowtie2/files/patch-Makefile')
| -rw-r--r-- | biology/bowtie2/files/patch-Makefile | 31 |
1 files changed, 29 insertions, 2 deletions
diff --git a/biology/bowtie2/files/patch-Makefile b/biology/bowtie2/files/patch-Makefile index be8a43586cec..6c4919530320 100644 --- a/biology/bowtie2/files/patch-Makefile +++ b/biology/bowtie2/files/patch-Makefile @@ -1,4 +1,4 @@ ---- Makefile.orig 2016-02-11 17:20:57 UTC +--- Makefile.orig 2016-12-30 15:40:06 UTC +++ Makefile @@ -21,8 +21,8 @@ # Makefile for bowtie, bowtie2-build, bowtie2-inspect @@ -11,7 +11,34 @@ INC = GCC_PREFIX = $(shell dirname `which gcc`) -@@ -169,7 +169,7 @@ SSE_FLAG=-msse2 +@@ -62,6 +62,8 @@ ifeq (1, $(POPCNT_CAPABILITY)) + INC += -I third_party + endif + ++INC += -I ${LOCALBASE}/include ++ + MM_DEF = + + ifeq (1,$(BOWTIE_MM)) +@@ -75,7 +77,7 @@ ifeq (1,$(BOWTIE_SHARED_MEM)) + endif + + PTHREAD_PKG = +-PTHREAD_LIB = ++PTHREAD_LIB = + + #if we're not using TBB, then we can't use queuing locks + ifeq (1,$(NO_TBB)) +@@ -94,7 +96,7 @@ endif + + #default is to use Intel TBB + ifneq (1,$(NO_TBB)) +- LIBS = $(PTHREAD_LIB) -ltbb -ltbbmalloc_proxy ++ LIBS = $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc + override EXTRA_FLAGS += -DWITH_TBB + else + LIBS = $(PTHREAD_LIB) +@@ -185,7 +187,7 @@ SSE_FLAG=-msse2 DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG) DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" |