Index: head/biology/bowtie2/Makefile =================================================================== --- head/biology/bowtie2/Makefile (revision 455160) +++ head/biology/bowtie2/Makefile (revision 455161) @@ -1,46 +1,44 @@ -# 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 OPTIONS_DEFINE= DOCS EXAMPLES post-install: ${MKDIR} ${STAGEDIR}${DATADIR}/scripts ${INSTALL_PROGRAM} \ ${WRKSRC}/bowtie2*-s \ ${WRKSRC}/bowtie2*-l \ ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} \ ${WRKSRC}/scripts/*.sh \ ${WRKSRC}/scripts/*.pl \ ${STAGEDIR}${DATADIR}/scripts post-install-DOCS-on: (cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) post-install-EXAMPLES-on: (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) .include Index: head/biology/bowtie2/distinfo =================================================================== --- head/biology/bowtie2/distinfo (revision 455160) +++ head/biology/bowtie2/distinfo (revision 455161) @@ -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 Index: head/biology/bowtie2/files/patch-aligner__result.cpp =================================================================== --- head/biology/bowtie2/files/patch-aligner__result.cpp (revision 455160) +++ head/biology/bowtie2/files/patch-aligner__result.cpp (nonexistent) @@ -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); Property changes on: head/biology/bowtie2/files/patch-aligner__result.cpp ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/biology/bowtie2/files/patch-Makefile =================================================================== --- head/biology/bowtie2/files/patch-Makefile (revision 455160) +++ head/biology/bowtie2/files/patch-Makefile (revision 455161) @@ -1,49 +1,34 @@ ---- 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 # -prefix = /usr/local -bindir = $(prefix)/bin +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 + GCC_SUFFIX = +@@ -98,7 +99,7 @@ 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 +- 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)\"" -RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3 +RELEASE_FLAGS = $(CXXFLAGS) $(SSE_FLAG) -funroll-loops RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" NOASSERT_FLAGS = -DNDEBUG FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE Index: head/biology/bowtie2/pkg-plist =================================================================== --- head/biology/bowtie2/pkg-plist (revision 455160) +++ head/biology/bowtie2/pkg-plist (revision 455161) @@ -1,64 +1,63 @@ bin/bowtie2 bin/bowtie2-align-l bin/bowtie2-align-s bin/bowtie2-build bin/bowtie2-build-l bin/bowtie2-build-s bin/bowtie2-inspect bin/bowtie2-inspect-l bin/bowtie2-inspect-s %%DATADIR%%/scripts/convert_quals.pl %%DATADIR%%/scripts/gen_2b_occ_lookup.pl %%DATADIR%%/scripts/gen_occ_lookup.pl %%DATADIR%%/scripts/gen_solqual_lookup.pl %%DATADIR%%/scripts/infer_fraglen.pl %%DATADIR%%/scripts/make_a_thaliana_tair.sh %%DATADIR%%/scripts/make_b_taurus_UMD3.sh %%DATADIR%%/scripts/make_c_elegans.sh %%DATADIR%%/scripts/make_canFam2.sh %%DATADIR%%/scripts/make_d_melanogaster.sh %%DATADIR%%/scripts/make_e_coli.sh %%DATADIR%%/scripts/make_h_sapiens_ncbi36.sh %%DATADIR%%/scripts/make_h_sapiens_ncbi37.sh %%DATADIR%%/scripts/make_hg18.sh %%DATADIR%%/scripts/make_hg19.sh %%DATADIR%%/scripts/make_m_musculus_ncbi37.sh %%DATADIR%%/scripts/make_mm10.sh %%DATADIR%%/scripts/make_mm9.sh %%DATADIR%%/scripts/make_rn4.sh %%DATADIR%%/scripts/make_s_cerevisiae.sh %%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/images/bowtie_logo.png %%PORTDOCS%%%%DOCSDIR%%/images/osi-certified.gif %%PORTDOCS%%%%DOCSDIR%%/images/sflogo.png %%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 %%PORTDOCS%%%%DOCSDIR%%/website/foot.ssi %%PORTDOCS%%%%DOCSDIR%%/website/index.html %%PORTDOCS%%%%DOCSDIR%%/website/index.shtml %%PORTDOCS%%%%DOCSDIR%%/website/manual.shtml %%PORTDOCS%%%%DOCSDIR%%/website/manual.ssi %%PORTDOCS%%%%DOCSDIR%%/website/news.shtml %%PORTDOCS%%%%DOCSDIR%%/website/old_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/other_tools.shtml %%PORTDOCS%%%%DOCSDIR%%/website/push.sh %%PORTDOCS%%%%DOCSDIR%%/website/push_images.sh %%PORTDOCS%%%%DOCSDIR%%/website/recent_news.ssi %%PORTDOCS%%%%DOCSDIR%%/website/rhsidebar.ssi %%PORTDOCS%%%%DOCSDIR%%/website/top.ssi %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.1.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.2.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.3.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.4.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.1.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.2.bt2 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/longreads.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_1.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_2.fq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/simulate.pl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/reference/lambda_virus.fa