Index: head/biology/bcftools/Makefile =================================================================== --- head/biology/bcftools/Makefile (revision 544089) +++ head/biology/bcftools/Makefile (revision 544090) @@ -1,66 +1,64 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= bcftools PORTVERSION= 1.9 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= cartwright@asu.edu COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= htslib>=1.6:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash - -CONFLICTS_BUILD=openssl USES= autoreconf gmake localbase \ perl5 python:env shebangfix USE_GITHUB= yes GH_ACCOUNT= samtools USE_LDCONFIG= ${PREFIX}/libexec/${PORTNAME} USE_PERL5= test GNU_CONFIGURE= yes SHEBANG_FILES= misc/* test/test.pl OPTIONS_DEFINE= GPL GPL_DESC= Enable modules that rely on GPL code OPTIONS_DEFAULT= GPL GPL_LIB_DEPENDS= libgsl.so:math/gsl .include .if ${PORT_OPTIONS:MGPL} MAKE_ENV+= USE_GPL=1 LICENSE+= GPLv3 LICENSE_COMB= multi .endif TEST_TARGET= test post-patch: @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac post-install: ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \ ${STAGEDIR}${PREFIX}/bin/color-chrs ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\ ${STAGEDIR}${PREFIX}/bin/guess-ploidy ${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \ ${STAGEDIR}${PREFIX}/bin/plot-roh ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \ ${STAGEDIR}${PREFIX}/bin/run-roh ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \ ${STAGEDIR}${PREFIX}/bin/vcfutils ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \ ${STAGEDIR}${PREFIX}/bin/ ${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/ .include Index: head/biology/cufflinks/Makefile =================================================================== --- head/biology/cufflinks/Makefile (revision 544089) +++ head/biology/cufflinks/Makefile (revision 544090) @@ -1,43 +1,44 @@ # $FreeBSD$ PORTNAME= cufflinks DISTVERSIONPREFIX= v DISTVERSION= 2.2.1-89 +PORTREVISION= 1 DISTVERSIONSUFFIX= -gdc3b0cb CATEGORIES= biology PATCH_SITES= https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/ PATCHFILES+= ea4671149f3054c773d99cea521db75bf7b0658f.patch:-p1 # https://github.com/cole-trapnell-lab/cufflinks/pull/127 MAINTAINER= yuri@FreeBSD.org COMMENT= Cufflinks assembles transcripts, estimates their abundance, etc LICENSE= BSL LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libhts.so:biology/htslib USES= autoreconf compiler:c++11-lang eigen:3 gmake python shebangfix SHEBANG_FILES= src/cuffmerge GNU_CONFIGURE= yes USE_GITHUB= yes GH_ACCOUNT= cole-trapnell-lab CXXFLAGS+= -I${LOCALBASE}/include/eigen3 CFLAGS+= -I${LOCALBASE}/include/eigen3 # https://github.com/cole-trapnell-lab/cufflinks/issues/113 PLIST_FILES= bin/compress_gtf \ bin/cuffcompare \ bin/cuffdiff \ bin/cufflinks \ bin/cuffmerge \ bin/cuffnorm \ bin/cuffquant \ bin/gffread \ bin/gtf_to_sam post-patch: # https://github.com/cole-trapnell-lab/cufflinks/issues/116 @${GREP} -rl 'fabs(' ${WRKSRC} | ${GREP} "\.cpp$$" | ${XARGS} ${REINPLACE_CMD} 's|std::fabs(|fabs(| ; s|fabs(|::fabs(|' .include Index: head/biology/htslib/Makefile =================================================================== --- head/biology/htslib/Makefile (revision 544089) +++ head/biology/htslib/Makefile (revision 544090) @@ -1,40 +1,40 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= htslib -DISTVERSION= 1.9 +DISTVERSION= 1.10.2 CATEGORIES= biology devel -MAINTAINER= cartwright@asu.edu +MAINTAINER= jwb@FreeBSD.org COMMENT= C library for high-throughput sequencing data formats LICENSE= BSD3CLAUSE MIT LICENSE_COMB= multi LICENSE_FILE= ${WRKSRC}/LICENSE +LIB_DEPENDS= libdeflate.so:archivers/libdeflate TEST_DEPENDS= bash:shells/bash -USES= autoreconf gmake localbase \ - pathfix perl5 shebangfix +USES= autoreconf gmake localbase pathfix perl5 shebangfix USE_GITHUB= yes -GH_ACCOUNT= samtools USE_PERL5= test USE_LDCONFIG= yes -GNU_CONFIGURE= yes + +GH_ACCOUNT= samtools +GNU_CONFIGURE= yes PATHFIX_MAKEFILEIN= Makefile -SHEBANG_FILES= test/compare_sam.pl \ - test/test.pl +SHEBANG_FILES= test/*.pl OPTIONS_DEFINE= CURL OPTIONS_DEFAULT= CURL CURL_DESC= Use libcurl for network file access (HTTPS and S3 support). CURL_USES= ssl CURL_LIB_DEPENDS= libcurl.so:ftp/curl CURL_CONFIGURE_ENABLE= libcurl PLIST_SUB= PORTVERSION="${PORTVERSION}" TEST_TARGET= test .include Index: head/biology/htslib/distinfo =================================================================== --- head/biology/htslib/distinfo (revision 544089) +++ head/biology/htslib/distinfo (revision 544090) @@ -1,3 +1,3 @@ -TIMESTAMP = 1532906408 -SHA256 (samtools-htslib-1.9_GH0.tar.gz) = d2e3cde77b8f874b37453c63390cd992901266336e9f70e871ef42402510467f -SIZE (samtools-htslib-1.9_GH0.tar.gz) = 1285580 +TIMESTAMP = 1595116892 +SHA256 (samtools-htslib-1.10.2_GH0.tar.gz) = b352eabed6392869dbdea0fe6db10a736a226d1f90036a724a49798f7e81cab7 +SIZE (samtools-htslib-1.10.2_GH0.tar.gz) = 1452177 Property changes on: head/biology/htslib/distinfo ___________________________________________________________________ Modified: fbsd:nokeywords ## -1 +1 ## -on \ No newline at end of property +yes \ No newline at end of property Index: head/biology/htslib/files/patch-Makefile =================================================================== --- head/biology/htslib/files/patch-Makefile (revision 544089) +++ head/biology/htslib/files/patch-Makefile (revision 544090) @@ -1,60 +1,66 @@ ---- Makefile.orig 2017-10-18 08:03:33 UTC +--- Makefile.orig 2020-08-02 22:52:13 UTC +++ Makefile -@@ -22,41 +22,26 @@ +@@ -22,25 +22,26 @@ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. -CC = gcc -AR = ar -RANLIB = ranlib -- --# Default libraries to link if configure is not used --htslib_default_libs = -lz -lm -lbz2 -llzma -- ++CC ?= gcc ++AR ?= ar ++RANLIB ?= ranlib + + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma -lcurl + -CPPFLAGS = --# TODO: probably update cram code to make it compile cleanly with -Wc++-compat --# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 --#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ --CFLAGS = -g -Wall -O2 ++# CPPFLAGS = + # TODO: make the 64-bit support for VCF optional via configure, for now add -DVCF_ALLOW_INT64 + # to CFLAGS manually, here or in config.mk if the latter exists. + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 +-CFLAGS = -g -Wall -O2 -fvisibility=hidden ++CFLAGS ?= -g -Wall -O2 -fvisibility=hidden EXTRA_CFLAGS_PIC = -fpic --LDFLAGS = --LIBS = $(htslib_default_libs) +-LDFLAGS = -fvisibility=hidden ++LDFLAGS ?= -fvisibility=hidden + LIBS = $(htslib_default_libs) -prefix = /usr/local -+prefix = ${PREFIX} ++PREFIX ?= /usr/local ++prefix = $(PREFIX) exec_prefix = $(prefix) bindir = $(exec_prefix)/bin includedir = $(prefix)/include - libdir = $(exec_prefix)/lib - libexecdir = $(exec_prefix)/libexec - datarootdir = $(prefix)/share --mandir = $(datarootdir)/man -+mandir = $(prefix)/man - man1dir = $(mandir)/man1 - man5dir = $(mandir)/man5 +@@ -53,13 +54,13 @@ man5dir = $(mandir)/man5 + man7dir = $(mandir)/man7 pkgconfigdir= $(prefix)/libdata/pkgconfig - MKDIR_P = mkdir -p +-MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 -INSTALL_LIB = $(INSTALL_DATA) -INSTALL_MAN = $(INSTALL_DATA) -INSTALL_PROGRAM = $(INSTALL) ++# Use ports BSD_INSTALL_PROGRAM to strip if WITH_DEBUG is not set ++MKDIR_P = mkdir -p +INSTALL_DATA = ${BSD_INSTALL_DATA} +INSTALL_DIR = $(MKDIR_P) +INSTALL_LIB = ${BSD_INSTALL_LIB} +INSTALL_MAN = ${BSD_INSTALL_MAN} +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} # Set by config.mk if plugins are enabled plugindir = -@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \ - test/thrash_threads5 \ - test/thrash_threads6 +@@ -98,7 +99,7 @@ BUILT_THRASH_PROGRAMS = \ + test/thrash_threads6 \ + test/thrash_threads7 -all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) +all: lib-static lib-shared $(BUILT_PROGRAMS) plugins HTSPREFIX = include htslib_vars.mk Index: head/biology/htslib/files/patch-hfile__libcurl.c =================================================================== --- head/biology/htslib/files/patch-hfile__libcurl.c (revision 544089) +++ head/biology/htslib/files/patch-hfile__libcurl.c (revision 544090) @@ -1,13 +1,74 @@ ---- hfile_libcurl.c.orig 2017-09-28 11:20:23 UTC +--- hfile_libcurl.c.orig 2019-12-19 09:54:30 UTC +++ hfile_libcurl.c -@@ -49,6 +49,10 @@ typedef struct { +@@ -74,6 +74,10 @@ typedef struct { unsigned int size; } hdrlist; +#ifndef ENOTRECOVERABLE +#define ENOTRECOVERABLE EIO +#endif + typedef struct { hdrlist fixed; // List of headers supplied at hopen() hdrlist extra; // List of headers from callback +@@ -218,6 +222,8 @@ static int easy_errno(CURL *easy, CURLcode err) + return EEXIST; + + default: ++ hts_log_error("Libcurl reported error %d (%s)", (int) err, ++ curl_easy_strerror(err)); + return EIO; + } + } +@@ -238,6 +244,8 @@ static int multi_errno(CURLMcode errm) + return ENOMEM; + + default: ++ hts_log_error("Libcurl reported error %d (%s)", (int) errm, ++ curl_multi_strerror(errm)); + return EIO; + } + } +@@ -797,9 +805,13 @@ static ssize_t libcurl_read(hFILE *fpv, void *bufferv, + fp->buffer.ptr.rd = buffer; + fp->buffer.len = nbytes; + fp->paused = 0; +- err = curl_easy_pause(fp->easy, CURLPAUSE_CONT); +- if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; } +- ++ if (! fp->finished) { ++ err = curl_easy_pause(fp->easy, CURLPAUSE_CONT); ++ if (err != CURLE_OK) { ++ errno = easy_errno(fp->easy, err); ++ return -1; ++ } ++ } + while (! fp->paused && ! fp->finished) { + if (wait_perform(fp) < 0) return -1; + } +@@ -1003,12 +1015,6 @@ static int restart_from_position(hFILE_libcurl *fp, of + } + temp_fp.nrunning = ++fp->nrunning; + +- err = curl_easy_pause(temp_fp.easy, CURLPAUSE_CONT); +- if (err != CURLE_OK) { +- save_errno = easy_errno(temp_fp.easy, err); +- goto error_remove; +- } +- + while (! temp_fp.paused && ! temp_fp.finished) + if (wait_perform(&temp_fp) < 0) { + save_errno = errno; +@@ -1084,8 +1090,10 @@ static int libcurl_close(hFILE *fpv) + fp->buffer.len = 0; + fp->closing = 1; + fp->paused = 0; +- err = curl_easy_pause(fp->easy, CURLPAUSE_CONT); +- if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err); ++ if (! fp->finished) { ++ err = curl_easy_pause(fp->easy, CURLPAUSE_CONT); ++ if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err); ++ } + + while (save_errno == 0 && ! fp->paused && ! fp->finished) + if (wait_perform(fp) < 0) save_errno = errno; Index: head/biology/htslib/pkg-plist =================================================================== --- head/biology/htslib/pkg-plist (revision 544089) +++ head/biology/htslib/pkg-plist (revision 544090) @@ -1,40 +1,41 @@ bin/bgzip bin/htsfile bin/tabix include/htslib/bgzf.h include/htslib/cram.h include/htslib/faidx.h include/htslib/hfile.h include/htslib/hts.h include/htslib/hts_defs.h include/htslib/hts_endian.h include/htslib/hts_log.h include/htslib/hts_os.h include/htslib/kbitset.h include/htslib/kfunc.h include/htslib/khash.h include/htslib/khash_str2int.h include/htslib/klist.h include/htslib/knetfile.h include/htslib/kseq.h include/htslib/ksort.h include/htslib/kstring.h include/htslib/regidx.h include/htslib/sam.h include/htslib/synced_bcf_reader.h include/htslib/tbx.h include/htslib/thread_pool.h include/htslib/vcf.h include/htslib/vcf_sweep.h include/htslib/vcfutils.h lib/libhts.a lib/libhts.so lib/libhts.so.%%PORTVERSION%% -lib/libhts.so.2 +lib/libhts.so.3 libdata/pkgconfig/htslib.pc man/man1/bgzip.1.gz man/man1/htsfile.1.gz man/man1/tabix.1.gz man/man5/faidx.5.gz man/man5/sam.5.gz man/man5/vcf.5.gz +man/man7/htslib-s3-plugin.7.gz Property changes on: head/biology/htslib/pkg-plist ___________________________________________________________________ Modified: fbsd:nokeywords ## -1 +1 ## -on \ No newline at end of property +yes \ No newline at end of property Index: head/biology/jellyfish/Makefile =================================================================== --- head/biology/jellyfish/Makefile (revision 544089) +++ head/biology/jellyfish/Makefile (revision 544090) @@ -1,45 +1,45 @@ # $FreeBSD$ PORTNAME= Jellyfish DISTVERSIONPREFIX= v DISTVERSION= 2.2.10 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Fast, memory-efficient counting of k-mers in DNA LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= yaggo:devel/yaggo LIB_DEPENDS= libhts.so:biology/htslib USES= autoreconf compiler:c++11-lib gmake libtool pathfix pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GNU_CONFIGURE= yes GH_ACCOUNT= gmarcais INSTALL_TARGET= install-strip PLIST_SUB= VER=${PORTVERSION} OPTIONS_DEFINE= NLS OPTIONS_SUB= yes NLS_USES= gettext NLS_CONFIGURE_ENABLE= nls .include # SSE code assumes amd64 features .if ${ARCH} != "amd64" CONFIGURE_ARGS+=--without-sse .endif .if ${CHOSEN_COMPILER_TYPE} == gcc CXXFLAGS+= -faligned-new .endif .include Index: head/biology/pbbam/Makefile =================================================================== --- head/biology/pbbam/Makefile (revision 544089) +++ head/biology/pbbam/Makefile (revision 544090) @@ -1,36 +1,36 @@ # $FreeBSD$ PORTNAME= pbbam DISTVERSION= 0.18.0 # Test with biology/unanimity before upgrading! -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology # As of March 2018, unanimity is no longer open source. # See https://github.com/PacificBiosciences/ccs. MAINTAINER= ports@FreeBSD.org COMMENT= PacBio BAM C++ library, with SWIG bindings LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libhts.so:biology/htslib \ libboost_regex.so:devel/boost-libs # Meson needs BOOST_ROOT=${LOCALBASE} # https://github.com/mesonbuild/meson/issues/2239 USES= compiler:c++14-lang localbase meson pkgconfig python USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= PacificBiosciences pre-configure: @${REINPLACE_CMD} -e "s|'python'|'${PYTHON_VERSION}'|g" \ ${WRKSRC}/meson.build post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/libpbbam.so.0.18 ${RLN} ${STAGEDIR}${PREFIX}/lib/libpbbam.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/libpbbam.so.0 .include Index: head/biology/samtools/Makefile =================================================================== --- head/biology/samtools/Makefile (revision 544089) +++ head/biology/samtools/Makefile (revision 544090) @@ -1,30 +1,31 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= samtools DISTVERSION= 1.9 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= cartwright@asu.edu COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= htslib>=1.6:biology/htslib LIB_DEPENDS= libhts.so:biology/htslib TEST_DEPENDS= bash:shells/bash USES= autoreconf gmake localbase ncurses \ perl5 python:env shebangfix USE_GITHUB= yes USE_PERL5= test GNU_CONFIGURE= yes SUB_FILES= pkg-message SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl TEST_TARGET= test .include Index: head/biology/tabixpp/Makefile =================================================================== --- head/biology/tabixpp/Makefile (revision 544089) +++ head/biology/tabixpp/Makefile (revision 544090) @@ -1,36 +1,37 @@ # $FreeBSD$ PORTNAME= tabixpp DISTVERSIONPREFIX= v DISTVERSION= 1.0.0-10 +PORTREVISION= 1 DISTVERSIONSUFFIX= -g6bbe690 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= C++ wrapper to tabix indexer LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libhts.so:biology/htslib USES= localbase:ldflags USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= ekg # Disable bundled htslib MAKE_ENV= HTS_HEADERS='' HTS_LIB='' MAKEFILE= ${FILESDIR}/Makefile INSTALL_TARGET= install-strip PLIST_FILES= bin/tabix++ \ include/tabix.hpp \ lib/libtabix.a \ lib/libtabix.so \ lib/libtabix.so.1 post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libtabix.so.1 \ ${STAGEDIR}${PREFIX}/lib/libtabix.so .include Index: head/biology/vcflib/Makefile =================================================================== --- head/biology/vcflib/Makefile (revision 544089) +++ head/biology/vcflib/Makefile (revision 544090) @@ -1,49 +1,50 @@ # $FreeBSD$ PORTNAME= vcflib DISTVERSIONPREFIX= v DISTVERSION= 1.0.0-rc1-130 +PORTREVISION= 1 DISTVERSIONSUFFIX= -g7e3d806 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= C++ library and CLI tools for parsing and manipulating VCF files LICENSE= MIT BROKEN_aarch64= fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? LIB_DEPENDS= libhts.so:biology/htslib \ libtabix.so:biology/tabixpp \ libsw.so:biology/smithwaterman COMMON_DEPENDS= fastahack:biology/fastahack \ filevercmp:sysutils/filevercmp \ fsom:science/fsom \ multichoose>=1.0.3:math/multichoose \ interval_tree_test:math/intervaltree BUILD_DEPENDS= ${COMMON_DEPENDS} RUN_DEPENDS= ${COMMON_DEPENDS} USES= gmake shebangfix USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= ekg CXXFLAGS+= -I${LOCALBASE}/include/smithwaterman \ -I${LOCALBASE}/include/multichoose \ -I${LOCALBASE}/include/filevercmp \ -I${LOCALBASE}/include/fastahack \ -I${LOCALBASE}/include/intervaltree \ -DVERSION='\"${PORTVERSION}\"' # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 MAKEFILE= ${FILESDIR}/Makefile.external-libs INSTALL_TARGET= install-strip post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libvcflib.so.1 \ ${STAGEDIR}${PREFIX}/lib/libvcflib.so .include