bowtie2: Upgrade to 2.3.4.2 and clean up
This commit is contained in:
Jason Bacon
parent
f1c68fe9f9
commit
39e47ee85c
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@ -5,11 +5,11 @@
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# Wed Mar 2 08:06:07 CST 2016 #
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###########################################################
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DISTNAME= bowtie2-${PORTVERSION}
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DISTNAME= bowtie2-${PV}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=BenLangmead/}
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GITHUB_PROJECT= bowtie2
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GITHUB_TAG= v${PORTVERSION}
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GITHUB_TAG= v${PV}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= http://bowtie-bio.sourceforge.net/index.shtml
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@ -21,12 +21,12 @@ USE_TOOLS+= gmake perl:run pax
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REPLACE_PERL= scripts/*.pl bowtie2
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REPLACE_PYTHON= bowtie2-build bowtie2-inspect
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PORTVERSION= 2.2.7
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PV= 2.3.4.2
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DATADIR= ${PREFIX}/share/bowtie2
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DOCSDIR= ${PREFIX}/share/doc/bowtie2
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EXAMPLESDIR= ${PREFIX}/share/examples/bowtie2
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INSTALLATION_DIRS= share/bowtie2/doc share/bowtie2/examples share/bowtie2/scripts
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INSTALLATION_DIRS= share/bowtie2/scripts
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post-install:
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${INSTALL_PROGRAM} \
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@ -45,4 +45,6 @@ post-install:
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cd ${WRKSRC}/doc && pax -rw * ${DESTDIR}${DOCSDIR}
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.include "../../lang/python/application.mk"
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.include "../../wip/tbb/buildlink3.mk"
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -36,7 +36,6 @@ share/doc/bowtie2/images/sflogo.png
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share/doc/bowtie2/images/university.small.horizontal.white.png
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share/doc/bowtie2/manual.html
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share/doc/bowtie2/release.txt
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share/doc/bowtie2/strip_markdown.pl
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share/doc/bowtie2/style.css
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share/doc/bowtie2/website/faq.shtml
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share/doc/bowtie2/website/faq.ssi
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@ -59,6 +58,7 @@ share/examples/bowtie2/index/lambda_virus.3.bt2
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share/examples/bowtie2/index/lambda_virus.4.bt2
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share/examples/bowtie2/index/lambda_virus.rev.1.bt2
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share/examples/bowtie2/index/lambda_virus.rev.2.bt2
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share/examples/bowtie2/reads/combined_reads.bam
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share/examples/bowtie2/reads/longreads.fq
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share/examples/bowtie2/reads/reads_1.fq
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share/examples/bowtie2/reads/reads_2.fq
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@ -1,8 +1,7 @@
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$NetBSD$
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SHA1 (bowtie2-2.2.7.tar.gz) = 001784d8a9e9fa06d705b2171af1309c30cf13e9
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RMD160 (bowtie2-2.2.7.tar.gz) = bf7af50df878a98ea84df70f3b1196d9b7ed5948
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SHA512 (bowtie2-2.2.7.tar.gz) = 5dc34d7fc9f31af0a648d2b6ec16e4a45679cf40569fdb69ba2f909aeed0b99b9cd364cbc8cfff8a7d011726fc53e7e7665f466cffaa27dd74ba5acd41b17d8d
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Size (bowtie2-2.2.7.tar.gz) = 5813850 bytes
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SHA1 (patch-Makefile) = de7328796af0997784e6ba37d3770aa57a149076
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SHA1 (patch-aligner__result.cpp) = 1c7ed81fdd4ac2decb27eac898286fc2284ddbae
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SHA1 (bowtie2-2.3.4.2.tar.gz) = 492434eac513cc480902b9ded2f3e70f0887f100
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RMD160 (bowtie2-2.3.4.2.tar.gz) = 582f4518db7a2eeb9178a404747586c2eb5b408b
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SHA512 (bowtie2-2.3.4.2.tar.gz) = eeb12569f3af9b45c702f47cf72e765cb060865365745e29a884b14df4ada33cf7d0b25f9e1c2680c12cbc0ab84d9d14b0910e53f992613508ede00edf14611e
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Size (bowtie2-2.3.4.2.tar.gz) = 10571530 bytes
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SHA1 (patch-Makefile) = 9b229a672d083deeb1be2ba8a42bcf342eb301c9
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@ -1,24 +1,25 @@
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$NetBSD$
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--- Makefile.orig 2016-02-11 17:20:57.000000000 +0000
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# Respect env
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--- Makefile.orig 2018-09-14 16:46:59.124139009 +0000
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+++ Makefile
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@@ -21,8 +21,8 @@
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# Makefile for bowtie, bowtie2-build, bowtie2-inspect
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#
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-prefix = /usr/local
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-bindir = $(prefix)/bin
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-prefix := /usr/local
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-bindir := $(prefix)/bin
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+PREFIX ?= /usr/local
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+bindir = $(PREFIX)/bin
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+bindir := $(PREFIX)/bin
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INC =
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GCC_PREFIX = $(shell dirname `which gcc`)
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@@ -169,7 +169,7 @@ SSE_FLAG=-msse2
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LDLIBS := -lz
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GCC_PREFIX := $(shell dirname `which gcc`)
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@@ -187,7 +187,7 @@ endif
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SSE_FLAG := -msse2
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DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG)
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
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-RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
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+RELEASE_FLAGS = ${CXXFLAGS} $(SSE_FLAG) -funroll-loops
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RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
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NOASSERT_FLAGS = -DNDEBUG
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FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
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DEBUG_FLAGS := -O0 -g3 -m64 $(SSE_FLAG)
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-RELEASE_FLAGS := -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
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+RELEASE_FLAGS := $(CXXFLAGS)
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NOASSERT_FLAGS := -DNDEBUG
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FILE_FLAGS := -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(CXXFLAGS)\""
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@ -1,11 +0,0 @@
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--- aligner_result.cpp.orig 2017-02-19 18:40:54.398991000 -0600
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+++ aligner_result.cpp 2017-02-19 18:41:14.093250000 -0600
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@@ -1130,7 +1130,7 @@ bool AlnFlags::printYF(BTString& o, bool
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else if(!nfilt_ ) flag = "NS";
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else if(!scfilt_ ) flag = "SC";
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else if(!qcfilt_ ) flag = "QC";
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- if(flag > 0) {
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+ if(*flag != '\0') {
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if(!first) o.append('\t');
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o.append("YF:Z:");
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o.append(flag);
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