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| author | jbeich <jbeich@FreeBSD.org> | 2017-02-27 22:08:30 +0800 |
|---|---|---|
| committer | jbeich <jbeich@FreeBSD.org> | 2017-02-27 22:08:30 +0800 |
| commit | cec3b9ef69fab58168f49aac772c6dfe5866bc64 (patch) | |
| tree | edec6243f10d8a9de988b7423bbe784205230990 /biology | |
| parent | f2071d3c45c01e34ded5e4d0c0ab9b1f1f646aef (diff) | |
| download | freebsd-ports-gnome-cec3b9ef69fab58168f49aac772c6dfe5866bc64.tar.gz freebsd-ports-gnome-cec3b9ef69fab58168f49aac772c6dfe5866bc64.tar.zst freebsd-ports-gnome-cec3b9ef69fab58168f49aac772c6dfe5866bc64.zip | |
biology/bowtie2: update to 2.3.0
- Unbreak with Clang 4.0
Changes: https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.0
PR: 216619
Submitted by: Jason Bacon <bacon4000@gmail.com> (maintainer)
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/bowtie2/Makefile | 4 | ||||
| -rw-r--r-- | biology/bowtie2/distinfo | 6 | ||||
| -rw-r--r-- | biology/bowtie2/files/patch-Makefile | 31 | ||||
| -rw-r--r-- | biology/bowtie2/files/patch-aligner__result.cpp | 13 |
4 files changed, 48 insertions, 6 deletions
diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile index a09862b29506..8ef489a65a53 100644 --- a/biology/bowtie2/Makefile +++ b/biology/bowtie2/Makefile @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= bowtie2 -PORTVERSION= 2.2.9 +PORTVERSION= 2.3.0 DISTVERSIONPREFIX= v CATEGORIES= biology @@ -12,6 +12,8 @@ COMMENT= Ultrafast, memory-efficient short read aligner LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE +LIB_DEPENDS+= libtbb.so:devel/tbb + # May also work on other 64-bit platforms, but untested ONLY_FOR_ARCHS= amd64 USES= gmake perl5 python shebangfix diff --git a/biology/bowtie2/distinfo b/biology/bowtie2/distinfo index 32a39c53fefa..2c1808146d4f 100644 --- a/biology/bowtie2/distinfo +++ b/biology/bowtie2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1475861880 -SHA256 (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = af940f77fc36aabea90d3d865724fd7ec7e250788d2d2f793c45c713d16ae5ee -SIZE (BenLangmead-bowtie2-v2.2.9_GH0.tar.gz) = 5815106 +TIMESTAMP = 1487550143 +SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221 +SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016 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)\"" diff --git a/biology/bowtie2/files/patch-aligner__result.cpp b/biology/bowtie2/files/patch-aligner__result.cpp new file mode 100644 index 000000000000..4a6c9f729522 --- /dev/null +++ b/biology/bowtie2/files/patch-aligner__result.cpp @@ -0,0 +1,13 @@ +https://github.com/BenLangmead/bowtie2/issues/81 + +--- aligner_result.cpp.orig 2016-12-30 15:40:06 UTC ++++ aligner_result.cpp +@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool + else if(!nfilt_ ) flag = "NS"; + else if(!scfilt_ ) flag = "SC"; + else if(!qcfilt_ ) flag = "QC"; +- if(flag > 0) { ++ if(*flag != '\0') { + if(!first) o.append('\t'); + o.append("YF:Z:"); + o.append(flag); |