svn commit: r544096 - in head/biology/bcftools: . files
Jason W. Bacon
jwb at FreeBSD.org
Mon Aug 3 18:16:56 UTC 2020
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 at asu.edu
+MAINTAINER= jwb at 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('', at 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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