Date: Thu, 5 Nov 2020 20:34:04 +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: r554157 - in head/biology/bcftools: . files Message-ID: <202011052034.0A5KY4OS038014@repo.freebsd.org>
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Author: jwb Date: Thu Nov 5 20:34:03 2020 New Revision: 554157 URL: https://svnweb.freebsd.org/changeset/ports/554157 Log: biology/bcftools: Upgrade to 1.11 Numerous new features, bug fixes and performance enhancements https://github.com/samtools/bcftools/releases/tag/1.11 Reported by: portscout Deleted: head/biology/bcftools/files/patch-misc_run-roh.pl 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 Thu Nov 5 20:32:39 2020 (r554156) +++ head/biology/bcftools/Makefile Thu Nov 5 20:34:03 2020 (r554157) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= bcftools -PORTVERSION= 1.10.2 +PORTVERSION= 1.11 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -13,6 +13,7 @@ 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 Modified: head/biology/bcftools/distinfo ============================================================================== --- head/biology/bcftools/distinfo Thu Nov 5 20:32:39 2020 (r554156) +++ head/biology/bcftools/distinfo Thu Nov 5 20:34:03 2020 (r554157) @@ -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 Modified: head/biology/bcftools/files/patch-Makefile ============================================================================== --- head/biology/bcftools/files/patch-Makefile Thu Nov 5 20:32:39 2020 (r554156) +++ head/biology/bcftools/files/patch-Makefile Thu Nov 5 20:34:03 2020 (r554157) @@ -1,26 +1,6 @@ ---- 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 @@ -30,18 +10,20 @@ 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} @@ -50,7 +32,7 @@ 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 @@ -59,12 +41,3 @@ 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) Modified: head/biology/bcftools/files/patch-test_test.pl ============================================================================== --- head/biology/bcftools/files/patch-test_test.pl Thu Nov 5 20:32:39 2020 (r554156) +++ head/biology/bcftools/files/patch-test_test.pl Thu Nov 5 20:34:03 2020 (r554157) @@ -1,24 +1,6 @@ ---- 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 = $$opts{bin}."/".$command; my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1"); @@ -27,7 +9,7 @@ my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg); -@@ -1118,7 +1118,7 @@ sub test_usage_subcommand +@@ -1291,7 +1291,7 @@ sub test_usage_subcommand my $subcommand = $args{subcmd}; my $commandpath = $$opts{bin}."/".$command; my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1"); Modified: head/biology/bcftools/pkg-plist ============================================================================== --- head/biology/bcftools/pkg-plist Thu Nov 5 20:32:39 2020 (r554156) +++ head/biology/bcftools/pkg-plist Thu Nov 5 20:34:03 2020 (r554157) @@ -1,5 +1,6 @@ bin/bcftools bin/color-chrs +bin/gff2gff.py bin/guess-ploidy bin/plot-roh bin/plot-vcfstats @@ -33,6 +34,7 @@ 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
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