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biology/bowtie2: Upgrade to 2.3.3.1

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Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13300
This commit is contained in:
Jason W. Bacon 2017-11-30 02:59:16 +00:00
parent f1f94f3166
commit 82d79438ee
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=455161
5 changed files with 19 additions and 50 deletions
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12
biology/bowtie2/Makefile
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@ -1,25 +1,23 @@
# Created by: Jason Bacon
# $FreeBSD$
PORTNAME= bowtie2
PORTVERSION= 2.3.0
PORTREVISION= 2
PORTVERSION= 2.3.3.1
DISTVERSIONPREFIX= v
CATEGORIES= biology
MAINTAINER= bacon4000@gmail.com
MAINTAINER= jwb@FreeBSD.org
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
LIB_DEPENDS= libtbb.so:devel/tbb
USES= gmake perl5 python shebangfix
USE_PERL5= run
SHEBANG_FILES= bowtie2-build bowtie2-inspect scripts/*.pl
SHEBANG_FILES= bowtie2-build bowtie2-inspect scripts/*.pl
USE_GITHUB= yes
GH_ACCOUNT= BenLangmead

6
biology/bowtie2/distinfo
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@ -1,3 +1,3 @@
TIMESTAMP = 1487550143
SHA256 (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 9804fddf36233f3f92c11e2250224de3395790cf35c8280c66387075df078221
SIZE (BenLangmead-bowtie2-v2.3.0_GH0.tar.gz) = 5810016
TIMESTAMP = 1511991430
SHA256 (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 8b9c0b9c595ebcddcac5feaf6acb44b2294d6deb91de107596ecad242a1a58e9
SIZE (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 5796279

37
biology/bowtie2/files/patch-Makefile
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@ -1,6 +1,6 @@
--- Makefile.orig 2016-12-30 15:40:06 UTC
--- Makefile.orig 2017-10-05 16:45:18 UTC
+++ Makefile
@@ -21,8 +21,8 @@
@@ -21,10 +21,11 @@
# Makefile for bowtie, bowtie2-build, bowtie2-inspect
#
@ -9,36 +9,21 @@
+PREFIX ?= /usr/local
+bindir = $(PREFIX)/bin
INC =
INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include)
+INC += -I${LOCALBASE}/include
LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
GCC_PREFIX = $(shell dirname `which gcc`)
@@ -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
GCC_SUFFIX =
@@ -98,7 +99,7 @@ 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
- LIBS += $(PTHREAD_LIB) -ltbb -ltbbmalloc$(if $(RELEASE_BUILD),,_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
LIBS += $(PTHREAD_LIB)
@@ -189,7 +190,7 @@ 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
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@ -1,13 +0,0 @@
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);

1
biology/bowtie2/pkg-plist
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@ -34,7 +34,6 @@ bin/bowtie2-inspect-s
%%PORTDOCS%%%%DOCSDIR%%/images/university.small.horizontal.white.png
%%PORTDOCS%%%%DOCSDIR%%/manual.html
%%PORTDOCS%%%%DOCSDIR%%/release.txt
%%PORTDOCS%%%%DOCSDIR%%/strip_markdown.pl
%%PORTDOCS%%%%DOCSDIR%%/style.css
%%PORTDOCS%%%%DOCSDIR%%/website/faq.shtml
%%PORTDOCS%%%%DOCSDIR%%/website/faq.ssi