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biology/bcftools: Upgrade to 1.11

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Numerous new features, bug fixes and performance enhancements
https://github.com/samtools/bcftools/releases/tag/1.11

Reported by:    portscout
This commit is contained in:
Jason W. Bacon 2020-11-05 20:34:03 +00:00
parent 025ca27d46
commit b0ab3ea009
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=554157
6 changed files with 18 additions and 71 deletions
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3
biology/bcftools/Makefile
View File

@ -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

6
biology/bcftools/distinfo
View File

@ -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

43
biology/bcftools/files/patch-Makefile
View File

@ -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)

11
biology/bcftools/files/patch-misc_run-roh.pl
View File

@ -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; }

24
biology/bcftools/files/patch-test_test.pl
View File

@ -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");

2
biology/bcftools/pkg-plist
View File

@ -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