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authorJustin <jlec@users.noreply.github.com>2013-09-26 23:27:37 -0700
committerJustin <jlec@users.noreply.github.com>2013-09-26 23:27:37 -0700
commitab0ec531115a2f8f46592210ed61ce02b91bf553 (patch)
treeef611bae246f9814378c6e4b88dc4cd420dec3d1 /sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
parentAdd sci-chemistry/openbabel-ruby live ebuild (diff)
parentsci-biology/bowtie: fixed check for sse2 support. (diff)
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Merge pull request #116 from cel4/master
sci-biology/bowtie: Added ebuild for bowtie-2.1.0.
Diffstat (limited to 'sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch')
-rw-r--r--sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch20
1 files changed, 20 insertions, 0 deletions
diff --git a/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
new file mode 100644
index 000000000..97300b1b0
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.1.0-buildsystem.patch
@@ -0,0 +1,20 @@
+--- Makefile.old 2013-09-22 12:07:12.606844000 +0200
++++ Makefile 2013-09-22 13:06:03.113888200 +0200
+@@ -24,8 +24,6 @@
+ INC =
+ GCC_PREFIX = $(shell dirname `which gcc`)
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+ CXX = $(CPP)
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1
+@@ -141,7 +139,7 @@
+
+ DEBUG_FLAGS = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
++RELEASE_FLAGS = $(CXXFLAGS)
+ RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE