Index: head/biology/bcftools/Makefile =================================================================== --- head/biology/bcftools/Makefile (revision 554156) +++ head/biology/bcftools/Makefile (revision 554157) @@ -1,61 +1,62 @@ # Created by: Reed A. Cartwright # $FreeBSD$ PORTNAME= bcftools -PORTVERSION= 1.10.2 +PORTVERSION= 1.11 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for manipulating next-generation sequencing data LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libhts.so.3:biology/htslib TEST_DEPENDS= bash:shells/bash +RUN_DEPENDS= bash:shells/bash USES= autoreconf gmake localbase perl5 python:env shebangfix USE_GITHUB= yes 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_DEFAULT= GPL GPL_LIB_DEPENDS= libgsl.so:math/gsl .include .if ${PORT_OPTIONS:MGPL} MAKE_ENV+= USE_GPL=1 LICENSE+= GPLv3 LICENSE_COMB= multi .endif TEST_TARGET= test pre-configure: @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \ ${WRKSRC}/configure.ac post-install: ${MV} ${STAGEDIR}${PREFIX}/bin/color-chrs.pl \ ${STAGEDIR}${PREFIX}/bin/color-chrs ${MV} ${STAGEDIR}${PREFIX}/bin/guess-ploidy.py\ ${STAGEDIR}${PREFIX}/bin/guess-ploidy ${MV} /${STAGEDIR}${PREFIX}/bin/plot-roh.py \ ${STAGEDIR}${PREFIX}/bin/plot-roh ${MV} ${STAGEDIR}${PREFIX}/bin/run-roh.pl \ ${STAGEDIR}${PREFIX}/bin/run-roh ${MV} ${STAGEDIR}${PREFIX}/bin/vcfutils.pl \ ${STAGEDIR}${PREFIX}/bin/vcfutils ${MV} ${STAGEDIR}${PREFIX}/bin/plot-vcfstats \ ${STAGEDIR}${PREFIX}/bin/ .include Index: head/biology/bcftools/distinfo =================================================================== --- head/biology/bcftools/distinfo (revision 554156) +++ head/biology/bcftools/distinfo (revision 554157) @@ -1,3 +1,3 @@ -TIMESTAMP = 1595166811 -SHA256 (samtools-bcftools-1.10.2_GH0.tar.gz) = 13277c17047152951e0bfe4467adc7768571b18e26610d206cab5560de5a395a -SIZE (samtools-bcftools-1.10.2_GH0.tar.gz) = 2880994 +TIMESTAMP = 1603028344 +SHA256 (samtools-bcftools-1.11_GH0.tar.gz) = f2d9a09fd7920754b60948b81ec047882864213b93a0cd1ef0372b0e025cba3f +SIZE (samtools-bcftools-1.11_GH0.tar.gz) = 3004923 Index: head/biology/bcftools/files/patch-misc_run-roh.pl =================================================================== --- head/biology/bcftools/files/patch-misc_run-roh.pl (revision 554156) +++ head/biology/bcftools/files/patch-misc_run-roh.pl (nonexistent) @@ -1,11 +0,0 @@ ---- misc/run-roh.pl.orig 2017-10-18 09:33:24 UTC -+++ misc/run-roh.pl -@@ -97,7 +97,7 @@ sub cmd - else - { - # child -- exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!"); -+ exec('/bin/sh', '-c', $cmd) or error("Failed to run the command [/bin/sh -c $cmd]: $!"); - } - - if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; } Property changes on: head/biology/bcftools/files/patch-misc_run-roh.pl ___________________________________________________________________ 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/bcftools/files/patch-Makefile =================================================================== --- head/biology/bcftools/files/patch-Makefile (revision 554156) +++ head/biology/bcftools/files/patch-Makefile (revision 554157) @@ -1,70 +1,43 @@ ---- Makefile.orig 2019-12-19 09:57:32 UTC +--- Makefile.orig 2020-10-18 13:31:52 UTC +++ Makefile -@@ -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 -O2 --LDFLAGS = --LIBS = -+CC ?= gcc -+AR ?= ar -+RANLIB ?= ranlib -+CPPFLAGS ?= -+CFLAGS ?= -g -Wall -O2 -+LDFLAGS ?= - - DYNAMIC_FLAGS = -rdynamic - PLUGINS_ENABLED = yes -@@ -45,7 +44,8 @@ OBJS = main.o vcfindex.o tabix.o \ +@@ -45,7 +45,8 @@ 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 ?= /usr/local +prefix = $(PREFIX) exec_prefix = $(prefix) bindir = $(exec_prefix)/bin libdir = $(exec_prefix)/lib -@@ -58,13 +58,13 @@ pluginpath = $(plugindir) +@@ -58,13 +59,14 @@ pluginpath = $(plugindir) # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) misc_bindir = $(bindir) -+# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set - MKDIR_P = mkdir -p +-MKDIR_P = mkdir -p -INSTALL = install -p -INSTALL_DATA = $(INSTALL) -m 644 -INSTALL_DIR = $(MKDIR_P) -m 755 -INSTALL_MAN = $(INSTALL_DATA) -INSTALL_PROGRAM = $(INSTALL) -INSTALL_SCRIPT = $(INSTALL_PROGRAM) ++# Use BSD_INSTALL_PROGRAM to strip when WITH_DEBUG not set ++MKDIR_P = mkdir -p ++INSTALL = install -p +INSTALL_DATA = ${BSD_INSTALL_DATA} +INSTALL_DIR = $(MKDIR_P) +INSTALL_MAN = ${BSD_INSTALL_MAN} +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} +INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} PROGRAMS = bcftools MISC_SCRIPTS = \ -@@ -141,7 +141,7 @@ print-version: +@@ -142,7 +144,7 @@ print-version: ifdef USE_GPL main.o : EXTRA_CPPFLAGS += -DUSE_GPL OBJS += polysomy.o peakfit.o - GSL_LIBS ?= -lgsl -lcblas + GSL_LIBS ?= -lgslcblas endif 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) -- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) -+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir) - $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir) - $(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir) Index: head/biology/bcftools/files/patch-test_test.pl =================================================================== --- head/biology/bcftools/files/patch-test_test.pl (revision 554156) +++ head/biology/bcftools/files/patch-test_test.pl (revision 554157) @@ -1,38 +1,20 @@ ---- test/test.pl.orig 2020-07-21 20:49:56 UTC +--- test/test.pl.orig 2020-10-18 13:36:42 UTC +++ test/test.pl -@@ -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('bash', '-o','pipefail','-c', $cmd) or error("Cannot execute the command [/usr/local/bin/sh -o pipefail -c $cmd]: $!"); - } - return ($? >> 8, join('',@out)); - } -@@ -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 +@@ -1236,7 +1236,7 @@ sub test_usage my $command = $args{cmd}; my $commandpath = $$opts{bin}."/".$command; my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1"); - if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; } + if ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; } my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); -@@ -1118,7 +1118,7 @@ sub test_usage_subcommand +@@ -1291,7 +1291,7 @@ sub test_usage_subcommand my $subcommand = $args{subcmd}; my $commandpath = $$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 ( $out =~ m/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath $subcommand: $out"); return; } my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); Index: head/biology/bcftools/pkg-plist =================================================================== --- head/biology/bcftools/pkg-plist (revision 554156) +++ head/biology/bcftools/pkg-plist (revision 554157) @@ -1,45 +1,47 @@ bin/bcftools bin/color-chrs +bin/gff2gff.py bin/guess-ploidy bin/plot-roh bin/plot-vcfstats bin/run-roh 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 libexec/bcftools/contrast.so libexec/bcftools/counts.so libexec/bcftools/dosage.so libexec/bcftools/fill-AN-AC.so libexec/bcftools/fill-from-fasta.so libexec/bcftools/fill-tags.so 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/scatter.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