Date: Mon, 3 Aug 2020 18:16:54 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r544096 - in head/biology/bcftools: . files Message-ID: <202008031816.073IGsID059625@repo.freebsd.org>
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Author: jwb Date: Mon Aug 3 18:16:54 2020 New Revision: 544096 URL: https://svnweb.freebsd.org/changeset/ports/544096 Log: biology/bcftools: Upgrade to 1.10.2 Numerous bug fixes and enhancements since 1.9: https://github.com/samtools/bcftools/tags Take maintainership per ports/248089. PR: ports/248089 Deleted: head/biology/bcftools/files/patch-prob1.c Modified: head/biology/bcftools/Makefile head/biology/bcftools/distinfo head/biology/bcftools/files/patch-Makefile head/biology/bcftools/files/patch-test_test.pl head/biology/bcftools/pkg-plist Modified: head/biology/bcftools/Makefile ============================================================================== --- head/biology/bcftools/Makefile Mon Aug 3 18:09:20 2020 (r544095) +++ head/biology/bcftools/Makefile Mon Aug 3 18:16:54 2020 (r544096) @@ -2,33 +2,30 @@ # $FreeBSD$ PORTNAME= bcftools -PORTVERSION= 1.9 -PORTREVISION= 2 +PORTVERSION= 1.10.2 CATEGORIES= biology -MAINTAINER= cartwright@asu.edu +MAINTAINER= jwb@FreeBSD.org 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 +LIB_DEPENDS= libhts.so.3:biology/htslib TEST_DEPENDS= bash:shells/bash -USES= autoreconf gmake localbase \ - perl5 python:env shebangfix +USES= autoreconf gmake localbase perl5 python:env shebangfix USE_GITHUB= yes -GH_ACCOUNT= samtools - USE_LDCONFIG= ${PREFIX}/libexec/${PORTNAME} USE_PERL5= test + +GH_ACCOUNT= samtools GNU_CONFIGURE= yes SHEBANG_FILES= misc/* test/test.pl -OPTIONS_DEFINE= GPL -GPL_DESC= Enable modules that rely on GPL code +OPTIONS_DEFINE= GPL +GPL_DESC= Enable modules that rely on GPL code OPTIONS_DEFAULT= GPL GPL_LIB_DEPENDS= libgsl.so:math/gsl @@ -43,22 +40,22 @@ LICENSE_COMB= multi TEST_TARGET= test -post-patch: - @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac +pre-configure: + @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \ + ${WRKSRC}/configure.ac post-install: - ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \ + ${MV} ${STAGEDIR}${PREFIX}/bin/color-chrs.pl \ ${STAGEDIR}${PREFIX}/bin/color-chrs - ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\ + ${MV} ${STAGEDIR}${PREFIX}/bin/guess-ploidy.py\ ${STAGEDIR}${PREFIX}/bin/guess-ploidy - ${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \ + ${MV} /${STAGEDIR}${PREFIX}/bin/plot-roh.py \ ${STAGEDIR}${PREFIX}/bin/plot-roh - ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \ + ${MV} ${STAGEDIR}${PREFIX}/bin/run-roh.pl \ ${STAGEDIR}${PREFIX}/bin/run-roh - ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \ + ${MV} ${STAGEDIR}${PREFIX}/bin/vcfutils.pl \ ${STAGEDIR}${PREFIX}/bin/vcfutils - ${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \ + ${MV} ${STAGEDIR}${PREFIX}/bin/plot-vcfstats \ ${STAGEDIR}${PREFIX}/bin/ - ${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/ .include <bsd.port.mk> Modified: head/biology/bcftools/distinfo ============================================================================== --- head/biology/bcftools/distinfo Mon Aug 3 18:09:20 2020 (r544095) +++ head/biology/bcftools/distinfo Mon Aug 3 18:16:54 2020 (r544096) @@ -1,3 +1,3 @@ -TIMESTAMP = 1532903716 -SHA256 (samtools-bcftools-1.9_GH0.tar.gz) = 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e -SIZE (samtools-bcftools-1.9_GH0.tar.gz) = 2394968 +TIMESTAMP = 1595166811 +SHA256 (samtools-bcftools-1.10.2_GH0.tar.gz) = 13277c17047152951e0bfe4467adc7768571b18e26610d206cab5560de5a395a +SIZE (samtools-bcftools-1.10.2_GH0.tar.gz) = 2880994 Modified: head/biology/bcftools/files/patch-Makefile ============================================================================== --- head/biology/bcftools/files/patch-Makefile Mon Aug 3 18:09:20 2020 (r544095) +++ head/biology/bcftools/files/patch-Makefile Mon Aug 3 18:16:54 2020 (r544096) @@ -1,40 +1,40 @@ ---- Makefile.orig 2018-07-18 08:34:29 UTC +--- Makefile.orig 2019-12-19 09:57:32 UTC +++ Makefile -@@ -22,10 +22,10 @@ +@@ -22,13 +22,12 @@ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # DEALINGS IN THE SOFTWARE. -CC = gcc +-AR = ar +-RANLIB = ranlib -CPPFLAGS = --CFLAGS = -g -Wall -Wc++-compat -O2 +-CFLAGS = -g -Wall -O2 -LDFLAGS = -+CC ?= cc -+CPPFLAGS += -+CFLAGS += -Wall -+LDFLAGS += - LIBS = +-LIBS = ++CC ?= gcc ++AR ?= ar ++RANLIB ?= ranlib ++CPPFLAGS ?= ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS ?= DYNAMIC_FLAGS = -rdynamic -@@ -42,26 +42,25 @@ OBJS = main.o vcfindex.o tabix.o \ - vcfsort.o \ + PLUGINS_ENABLED = yes +@@ -45,7 +44,8 @@ OBJS = main.o vcfindex.o tabix.o \ ccall.o em.o prob1.o kmin.o # the original samtools calling + PLUGIN_OBJS = vcfplugin.o -prefix = /usr/local -+prefix = ${PREFIX} ++PREFIX ?= /usr/local ++prefix = $(PREFIX) exec_prefix = $(prefix) bindir = $(exec_prefix)/bin libdir = $(exec_prefix)/lib - libexecdir = $(exec_prefix)/libexec --mandir = $(prefix)/share/man -+mandir = $(prefix)/man - man1dir = $(mandir)/man1 - # Installation location for $(PLUGINS) - plugindir = $(libexecdir)/bcftools - pluginpath = $(plugindir) +@@ -58,13 +58,13 @@ pluginpath = $(plugindir) # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) --misc_bindir = $(bindir) -+misc_bindir = $(bindir)/samtools_misc + misc_bindir = $(bindir) ++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_DATA = $(INSTALL) -m 644 @@ -50,25 +50,16 @@ PROGRAMS = bcftools MISC_SCRIPTS = \ -@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin - - ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) - ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS) --ALL_LIBS = -lz -ldl $(LIBS) -+ALL_LIBS = -lz $(LIBS) - - # Usually config.mk and config.h are generated by running configure - # or config.status, but if those aren't used create defaults here. -@@ -131,7 +130,7 @@ print-version: +@@ -141,7 +141,7 @@ print-version: ifdef USE_GPL main.o : EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o - GSL_LIBS ?= -lgsl -lcblas -+ GSL_LIBS ?= -lgsl -lgslcblas ++ GSL_LIBS ?= -lgslcblas endif - bcftools: $(OBJS) $(HTSLIB) -@@ -278,7 +277,7 @@ docs: doc/bcftools.1 doc/bcftools.html + print-%: +@@ -320,7 +320,7 @@ docs: doc/bcftools.1 doc/bcftools.html # Since there is no make dependency, bcftools.1 can be out-of-date and # make docs can be run to update if asciidoc is available install: $(PROGRAMS) $(PLUGINS) Modified: head/biology/bcftools/files/patch-test_test.pl ============================================================================== --- head/biology/bcftools/files/patch-test_test.pl Mon Aug 3 18:09:20 2020 (r544095) +++ head/biology/bcftools/files/patch-test_test.pl Mon Aug 3 18:16:54 2020 (r544096) @@ -1,29 +1,38 @@ ---- test/test.pl.orig 2017-10-18 09:33:24 UTC +--- test/test.pl.orig 2020-07-21 20:49:56 UTC +++ test/test.pl -@@ -381,7 +381,7 @@ sub _cmd +@@ -610,7 +610,7 @@ sub _cmd else { # child - exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!"); -+ exec('/usr/local/bin/bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!"); ++ exec('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!"); } return ($? >> 8, join('',@out)); } -@@ -782,7 +782,7 @@ sub test_usage +@@ -622,7 +622,7 @@ sub _cmd3 + my $pid = fork(); + if ( !$pid ) + { +- exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o"); ++ exec('bash', '-o','pipefail','-c', "($cmd) 2>$tmp.e >$tmp.o"); + } + waitpid($pid,0); + +@@ -1063,7 +1063,7 @@ sub test_usage my $command = $args{cmd}; my $commandpath = $$opts{bin}."/".$command; my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1"); - if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; } -+ if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; } ++ if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; } my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); -@@ -833,7 +833,7 @@ sub test_usage_subcommand +@@ -1118,7 +1118,7 @@ sub test_usage_subcommand my $subcommand = $args{subcmd}; my $commandpath = $$opts{bin}."/".$command; my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1"); - if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; } -+ if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; } ++ if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; } my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); Modified: head/biology/bcftools/pkg-plist ============================================================================== --- head/biology/bcftools/pkg-plist Mon Aug 3 18:09:20 2020 (r544095) +++ head/biology/bcftools/pkg-plist Mon Aug 3 18:16:54 2020 (r544096) @@ -8,7 +8,9 @@ bin/vcfutils libexec/bcftools/GTisec.so libexec/bcftools/GTsubset.so libexec/bcftools/ad-bias.so +libexec/bcftools/add-variantkey.so libexec/bcftools/af-dist.so +libexec/bcftools/allele-length.so libexec/bcftools/check-ploidy.so libexec/bcftools/check-sparsity.so libexec/bcftools/color-chrs.so @@ -22,15 +24,22 @@ libexec/bcftools/fixploidy.so libexec/bcftools/fixref.so libexec/bcftools/frameshifts.so libexec/bcftools/guess-ploidy.so +libexec/bcftools/gvcfz.so libexec/bcftools/impute-info.so +libexec/bcftools/indel-stats.so libexec/bcftools/isecGT.so libexec/bcftools/mendelian.so libexec/bcftools/missing2ref.so +libexec/bcftools/parental-origin.so libexec/bcftools/prune.so +libexec/bcftools/remove-overlaps.so libexec/bcftools/setGT.so libexec/bcftools/smpl-stats.so +libexec/bcftools/split-vep.so libexec/bcftools/split.so libexec/bcftools/tag2tag.so +libexec/bcftools/trio-dnm.so libexec/bcftools/trio-stats.so libexec/bcftools/trio-switch-rate.so +libexec/bcftools/variantkey-hex.so man/man1/bcftools.1.gz
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