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biology/bowtie2: update to 2.3.0

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- 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)
This commit is contained in:
Jan Beich 2017-02-27 14:08:30 +00:00
parent 45ad69e81c
commit fe0cf6e909
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=434940
4 changed files with 48 additions and 6 deletions
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4
biology/bowtie2/Makefile
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@ -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

6
biology/bowtie2/distinfo
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@ -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

31
biology/bowtie2/files/patch-Makefile
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@ -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)\""

13
biology/bowtie2/files/patch-aligner__result.cpp Normal file
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@ -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);