svn commit: r554157 - in head/biology/bcftools: . files
Jason W. Bacon
jwb at FreeBSD.org
Thu Nov 5 20:34:05 UTC 2020
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 at 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('', at 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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