svn commit: r452840 - in head/biology: bcftools bcftools/files htslib htslib/files samtools samtools/files
Luca Pizzamiglio
pizzamig at FreeBSD.org
Wed Oct 25 10:19:53 UTC 2017
Author: pizzamig
Date: Wed Oct 25 10:19:50 2017
New Revision: 452840
URL: https://svnweb.freebsd.org/changeset/ports/452840
Log:
biology/htslib biology/bcftools biology/samtools: Update to 1.6
PR: 223094
Submitted by: mzaki at niid.go.jp
Approved by: cartwright at asu.edu (maintainer)
Approved by: olivier (mentor)
Differential Revision: https://reviews.freebsd.org/D12768
Added:
head/biology/bcftools/files/patch-configure.ac (contents, props changed)
head/biology/bcftools/files/patch-misc_run-roh.pl (contents, props changed)
Deleted:
head/biology/htslib/files/patch-configure.ac
head/biology/samtools/files/ax_with_curses.m4
head/biology/samtools/files/ax_with_htslib.m4
head/biology/samtools/files/patch-configure.ac
head/biology/samtools/files/patch-dict.c
head/biology/samtools/files/patch-errmod.c
Modified:
head/biology/bcftools/Makefile
head/biology/bcftools/distinfo
head/biology/bcftools/files/patch-Makefile
head/biology/bcftools/files/patch-prob1.c
head/biology/bcftools/files/patch-test_test.pl
head/biology/bcftools/files/pkg-message.in
head/biology/bcftools/pkg-plist
head/biology/htslib/Makefile
head/biology/htslib/distinfo
head/biology/htslib/files/patch-Makefile
head/biology/htslib/files/patch-hfile__libcurl.c
head/biology/htslib/pkg-plist
head/biology/samtools/Makefile
head/biology/samtools/distinfo
head/biology/samtools/files/patch-Makefile
head/biology/samtools/files/patch-test_test.pl
head/biology/samtools/files/pkg-message.in
Modified: head/biology/bcftools/Makefile
==============================================================================
--- head/biology/bcftools/Makefile Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/bcftools/Makefile Wed Oct 25 10:19:50 2017 (r452840)
@@ -2,8 +2,7 @@
# $FreeBSD$
PORTNAME= bcftools
-PORTVERSION= 1.3.1
-PORTREVISION= 2
+PORTVERSION= 1.6
CATEGORIES= biology
MAINTAINER= cartwright at asu.edu
@@ -12,7 +11,7 @@ COMMENT= Tools for manipulating next-generation sequen
LICENSE= MIT
# LICENSE_FILE= ${WRKSRC}/LICENSE
-BUILD_DEPENDS= htslib>=1.3:biology/htslib
+BUILD_DEPENDS= htslib>=1.6:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash
@@ -21,10 +20,12 @@ CONFLICTS_BUILD=openssl
USE_GITHUB= yes
GH_ACCOUNT= samtools
-USES= gmake perl5 shebangfix
+USES= autoreconf gmake perl5 python shebangfix
USE_PERL5= test
+PYTHON_NO_DEPENDS= yes
+GNU_CONFIGURE= yes
SUB_FILES= pkg-message
-SHEBANG_FILES= vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
+SHEBANG_FILES= misc/* test/test.pl
OPTIONS_DEFINE= GPL
GPL_DESC= Enable modules that rely on GPL code
@@ -37,19 +38,15 @@ GPL_LIB_DEPENDS= libgsl.so:math/gsl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
-MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
- INSTALL_DATA="${INSTALL_DATA}" \
- INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
- INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
- INSTALL_DIR="${MKDIR}"
-
.if ${PORT_OPTIONS:MGPL}
MAKE_ENV+= USE_GPL=1
LICENSE= GPLv3
.endif
-PLIST_SUB= PORTVERSION="${PORTVERSION}"
-
TEST_TARGET= test
+
+post-patch:
+ @${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac || (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1)
+ @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
.include <bsd.port.mk>
Modified: head/biology/bcftools/distinfo
==============================================================================
--- head/biology/bcftools/distinfo Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/bcftools/distinfo Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1463692643
-SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e
-SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207
+TIMESTAMP = 1508307708
+SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025
+SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330
Modified: head/biology/bcftools/files/patch-Makefile
==============================================================================
--- head/biology/bcftools/files/patch-Makefile Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/bcftools/files/patch-Makefile Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,19 +1,9 @@
---- Makefile.orig 2015-12-15 21:42:34 UTC
+--- Makefile.orig 2017-09-28 11:22:48 UTC
+++ Makefile
-@@ -29,16 +29,15 @@ TEST_PROG= test/test-rbuf
- all: $(PROG) $(TEST_PROG)
+@@ -22,10 +22,10 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
- # Adjust $(HTSDIR) to point to your top-level htslib directory
--HTSDIR = ../htslib
--include $(HTSDIR)/htslib.mk
--HTSLIB = $(HTSDIR)/libhts.a
--BGZIP = $(HTSDIR)/bgzip
--TABIX = $(HTSDIR)/tabix
-+HTSDIR = $(prefix)/include
-+HTSLIB = -lhts
-+BGZIP = $(HTSDIR)/../bin/bgzip
-+TABIX = $(HTSDIR)/../bin/tabix
-
-CC = gcc
-CPPFLAGS =
-CFLAGS = -g -Wall -Wc++-compat -O2
@@ -24,17 +14,13 @@
+LDFLAGS +=
LIBS =
- OBJS = main.o vcfindex.o tabix.o \
-@@ -57,26 +56,20 @@ GSL_LIBS =
- ifdef USE_GPL
- EXTRA_CPPFLAGS += -DUSE_GPL
- OBJS += polysomy.o peakfit.o
-- GSL_LIBS = -lgsl -lcblas
-+ GSL_LIBS = -lgsl -lgslcblas
- endif
+ DYNAMIC_FLAGS = -rdynamic
+@@ -42,26 +42,25 @@ OBJS = main.o vcfindex.o tabix.o \
+ vcfsort.o \
+ ccall.o em.o prob1.o kmin.o # the original samtools calling
-prefix = /usr/local
-+prefix = ${STAGEDIR}${PREFIX}
++prefix = ${PREFIX}
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
libdir = $(exec_prefix)/lib
@@ -42,37 +28,52 @@
-mandir = $(prefix)/share/man
+mandir = $(prefix)/man
man1dir = $(mandir)/man1
-
+ # Installation location for $(PLUGINS)
plugindir = $(libexecdir)/bcftools
pluginpath = $(plugindir)
+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
+-misc_bindir = $(bindir)
++misc_bindir = $(bindir)/samtools_misc
--MKDIR_P = mkdir -p
+ MKDIR_P = mkdir -p
-INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
--
- MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
+-INSTALL_MAN = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
++INSTALL_DATA = ${BSD_INSTALL_DATA}
++INSTALL_DIR = $(MKDIR_P)
++INSTALL_MAN = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT}
- all:$(PROG) plugins
-@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
- $(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
+ PROGRAMS = bcftools
+ MISC_SCRIPTS = \
+@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
- bcftools: $(HTSLIB) $(OBJS)
-- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
-+ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)
+ ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS)
+-ALL_LIBS = -lz -ldl $(LIBS)
++ALL_LIBS = -lz $(LIBS)
- doc/bcftools.1: doc/bcftools.txt
- cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
-@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html
+ # 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:
+ ifdef USE_GPL
+ main.o : EXTRA_CPPFLAGS += -DUSE_GPL
+ OBJS += polysomy.o peakfit.o
+- GSL_LIBS ?= -lgsl -lcblas
++ GSL_LIBS ?= -lgsl -lgslcblas
+ endif
+
+ bcftools: $(OBJS) $(HTSLIB)
+@@ -273,7 +272,7 @@ 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: $(PROG)
+ install: $(PROG) $(PLUGINS)
- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
-- $(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
-+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
-+ $(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)
-+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
- $(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
- $(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(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)
Added: head/biology/bcftools/files/patch-configure.ac
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bcftools/files/patch-configure.ac Wed Oct 25 10:19:50 2017 (r452840)
@@ -0,0 +1,11 @@
+--- configure.ac.orig 2017-09-28 11:22:48 UTC
++++ configure.ac
+@@ -23,7 +23,7 @@
+ # DEALINGS IN THE SOFTWARE.
+
+ dnl Process this file with autoconf to produce a configure script
+-AC_INIT([BCFtools], m4_esyscmd_s([make print-version]),
++AC_INIT([BCFtools], [@PORTVERSION@],
+ [samtools-help at lists.sourceforge.net], [], [http://www.htslib.org/])
+ AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER
+ AC_CONFIG_SRCDIR([main.c])
Added: head/biology/bcftools/files/patch-misc_run-roh.pl
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/bcftools/files/patch-misc_run-roh.pl Wed Oct 25 10:19:50 2017 (r452840)
@@ -0,0 +1,11 @@
+--- 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}) && !$args{exit_on_error} ) { return @out; }
Modified: head/biology/bcftools/files/patch-prob1.c
==============================================================================
--- head/biology/bcftools/files/patch-prob1.c Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/bcftools/files/patch-prob1.c Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,4 +1,4 @@
---- prob1.c.orig 2015-12-15 21:42:34 UTC
+--- prob1.c.orig 2017-09-28 11:22:48 UTC
+++ prob1.c
@@ -33,6 +33,12 @@ THE SOFTWARE. */
#include <zlib.h>
Modified: head/biology/bcftools/files/patch-test_test.pl
==============================================================================
--- head/biology/bcftools/files/patch-test_test.pl Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/bcftools/files/patch-test_test.pl Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,6 +1,6 @@
---- test/test.pl.orig 2015-12-22 22:45:13 UTC
+--- test/test.pl.orig 2017-10-18 09:33:24 UTC
+++ test/test.pl
-@@ -290,7 +290,7 @@ sub _cmd
+@@ -381,7 +381,7 @@ sub _cmd
else
{
# child
@@ -9,7 +9,7 @@
}
return ($? >> 8, join('', at out));
}
-@@ -657,7 +657,7 @@ sub test_usage
+@@ -782,7 +782,7 @@ sub test_usage
my $command = $args{cmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
@@ -18,7 +18,7 @@
my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
-@@ -708,7 +708,7 @@ sub test_usage_subcommand
+@@ -833,7 +833,7 @@ sub test_usage_subcommand
my $subcommand = $args{subcmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");
Modified: head/biology/bcftools/files/pkg-message.in
==============================================================================
--- head/biology/bcftools/files/pkg-message.in Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/bcftools/files/pkg-message.in Wed Oct 25 10:19:50 2017 (r452840)
@@ -3,5 +3,5 @@ The miscellaneous tools included with Bcftools have be
Add that directory to your path if you want to use these tools.
-Some of these tools depend on Perl5, and it will need to be installed to
+Some of these tools depend on Perl5/Python, and it will need to be installed to
use them.
Modified: head/biology/bcftools/pkg-plist
==============================================================================
--- head/biology/bcftools/pkg-plist Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/bcftools/pkg-plist Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,19 +1,32 @@
bin/bcftools
bin/samtools_misc/color-chrs.pl
+bin/samtools_misc/guess-ploidy.py
+bin/samtools_misc/plot-roh.py
bin/samtools_misc/plot-vcfstats
+bin/samtools_misc/run-roh.pl
bin/samtools_misc/vcfutils.pl
libexec/bcftools/GTisec.so
+libexec/bcftools/GTsubset.so
+libexec/bcftools/ad-bias.so
+libexec/bcftools/af-dist.so
+libexec/bcftools/check-ploidy.so
+libexec/bcftools/check-sparsity.so
libexec/bcftools/color-chrs.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/impute-info.so
+libexec/bcftools/isecGT.so
libexec/bcftools/mendelian.so
libexec/bcftools/missing2ref.so
+libexec/bcftools/prune.so
libexec/bcftools/setGT.so
libexec/bcftools/tag2tag.so
-libexec/bcftools/vcf2sex.so
+libexec/bcftools/trio-switch-rate.so
man/man1/bcftools.1.gz
Modified: head/biology/htslib/Makefile
==============================================================================
--- head/biology/htslib/Makefile Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/htslib/Makefile Wed Oct 25 10:19:50 2017 (r452840)
@@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= htslib
-PORTVERSION= 1.3.1
+PORTVERSION= 1.6
CATEGORIES= biology devel
MAINTAINER= cartwright at asu.edu
@@ -34,16 +34,8 @@ CURL_CONFIGURE_ENABLE= libcurl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
-MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
- INSTALL_DATA="${INSTALL_DATA}" \
- INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
- INSTALL_DIR="${MKDIR}"
-
PLIST_SUB= PORTVERSION="${PORTVERSION}"
TEST_TARGET= test
-
-post-patch:
- @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
.include <bsd.port.mk>
Modified: head/biology/htslib/distinfo
==============================================================================
--- head/biology/htslib/distinfo Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/htslib/distinfo Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1463688817
-SHA256 (samtools-htslib-1.3.1_GH0.tar.gz) = 3bbd04f9a0c4c301abd5d19a81920894ac2ee5e86e8aa977e8c2035e01d93ea7
-SIZE (samtools-htslib-1.3.1_GH0.tar.gz) = 1065840
+TIMESTAMP = 1508301522
+SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6
+SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672
Modified: head/biology/htslib/files/patch-Makefile
==============================================================================
--- head/biology/htslib/files/patch-Makefile Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/htslib/files/patch-Makefile Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,6 +1,6 @@
---- Makefile.orig 2016-04-22 08:45:12 UTC
+--- Makefile.orig 2017-10-18 08:03:33 UTC
+++ Makefile
-@@ -22,16 +22,7 @@
+@@ -22,41 +22,26 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
@@ -8,16 +8,23 @@
-AR = ar
-RANLIB = ranlib
-
+-# Default libraries to link if configure is not used
+-htslib_default_libs = -lz -lm -lbz2 -llzma
+-
-CPPFLAGS =
-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+-# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
-CFLAGS = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS =
--LIBS =
+-LIBS = $(htslib_default_libs)
- # For now these don't work too well as samtools also needs to know to
- # add -lbz2 and -llzma if linking against the static libhts.a library.
-@@ -58,17 +49,11 @@ includedir = $(prefix)/include
+-prefix = /usr/local
++prefix = ${PREFIX}
+ exec_prefix = $(prefix)
+ bindir = $(exec_prefix)/bin
+ includedir = $(prefix)/include
libdir = $(exec_prefix)/lib
libexecdir = $(exec_prefix)/libexec
datarootdir = $(prefix)/share
@@ -27,30 +34,27 @@
man5dir = $(mandir)/man5
pkgconfigdir= $(prefix)/libdata/pkgconfig
--MKDIR_P = mkdir -p
+ MKDIR_P = mkdir -p
-INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
--
+-INSTALL_LIB = $(INSTALL_DATA)
+-INSTALL_MAN = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
++INSTALL_DATA = ${BSD_INSTALL_DATA}
++INSTALL_DIR = $(MKDIR_P)
++INSTALL_LIB = ${BSD_INSTALL_LIB}
++INSTALL_MAN = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+
# Set by config.mk if plugins are enabled
plugindir =
+@@ -87,7 +72,7 @@ BUILT_THRASH_PROGRAMS = \
+ test/thrash_threads5 \
+ test/thrash_threads6
-@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
- test/test-vcf-api \
- test/test-vcf-sweep
-
-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
HTSPREFIX =
include htslib_vars.mk
-@@ -360,7 +345,7 @@ installdirs:
- # and libhts.so.NN (used by client executables at runtime).
-
- install-so: libhts.so installdirs
-- $(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
-+ $(INSTALL_LIB) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
- ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
- ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
-
Modified: head/biology/htslib/files/patch-hfile__libcurl.c
==============================================================================
--- head/biology/htslib/files/patch-hfile__libcurl.c Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/htslib/files/patch-hfile__libcurl.c Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,13 +1,13 @@
---- hfile_libcurl.c.orig 2015-12-15 16:34:33 UTC
+--- hfile_libcurl.c.orig 2017-09-28 11:20:23 UTC
+++ hfile_libcurl.c
-@@ -39,6 +39,10 @@ DEALINGS IN THE SOFTWARE. */
+@@ -49,6 +49,10 @@ typedef struct {
+ unsigned int size;
+ } hdrlist;
- #include <curl/curl.h>
-
+#ifndef ENOTRECOVERABLE
+#define ENOTRECOVERABLE EIO
+#endif
+
typedef struct {
- hFILE base;
- CURL *easy;
+ hdrlist fixed; // List of headers supplied at hopen()
+ hdrlist extra; // List of headers from callback
Modified: head/biology/htslib/pkg-plist
==============================================================================
--- head/biology/htslib/pkg-plist Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/htslib/pkg-plist Wed Oct 25 10:19:50 2017 (r452840)
@@ -7,6 +7,9 @@ include/htslib/faidx.h
include/htslib/hfile.h
include/htslib/hts.h
include/htslib/hts_defs.h
+include/htslib/hts_endian.h
+include/htslib/hts_log.h
+include/htslib/hts_os.h
include/htslib/kbitset.h
include/htslib/kfunc.h
include/htslib/khash.h
@@ -20,13 +23,14 @@ include/htslib/regidx.h
include/htslib/sam.h
include/htslib/synced_bcf_reader.h
include/htslib/tbx.h
+include/htslib/thread_pool.h
include/htslib/vcf.h
include/htslib/vcf_sweep.h
include/htslib/vcfutils.h
lib/libhts.a
lib/libhts.so
-lib/libhts.so.1
lib/libhts.so.%%PORTVERSION%%
+lib/libhts.so.2
libdata/pkgconfig/htslib.pc
man/man1/htsfile.1.gz
man/man1/tabix.1.gz
Modified: head/biology/samtools/Makefile
==============================================================================
--- head/biology/samtools/Makefile Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/samtools/Makefile Wed Oct 25 10:19:50 2017 (r452840)
@@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= samtools
-PORTVERSION= 1.3.1
+PORTVERSION= 1.6
CATEGORIES= biology
MAINTAINER= cartwright at asu.edu
@@ -11,34 +11,22 @@ COMMENT= Tools for manipulating next-generation sequen
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
-BUILD_DEPENDS= htslib>=1.3:biology/htslib
+BUILD_DEPENDS= htslib>=1.6:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
TEST_DEPENDS= bash:shells/bash
USE_GITHUB= yes
-USES= autoreconf gmake ncurses perl5 shebangfix
+USES= autoreconf gmake ncurses perl5 python shebangfix
USE_PERL5= test
+PYTHON_NO_DEPENDS= yes
GNU_CONFIGURE= yes
SUB_FILES= pkg-message
-SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl
+SHEBANG_FILES= misc/*.pl misc/*.py misc/plot-bamstats test/test.pl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
-MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
- INSTALL_DATA="${INSTALL_DATA}" \
- INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
- INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
- INSTALL_DIR="${MKDIR}"
-
-PLIST_SUB= PORTVERSION="${PORTVERSION}"
-
TEST_TARGET= test
-
-post-patch:
- @${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac
- ${CP} ${FILESDIR}/ax_with_htslib.m4 ${WRKSRC}/
- ${CP} ${FILESDIR}/ax_with_curses.m4 ${WRKSRC}/
.include <bsd.port.mk>
Modified: head/biology/samtools/distinfo
==============================================================================
--- head/biology/samtools/distinfo Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/samtools/distinfo Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1463691050
-SHA256 (samtools-samtools-1.3.1_GH0.tar.gz) = 30752c7b92cd9e146f4017983b2a41beb58c8966e93572cea76a14719f95a768
-SIZE (samtools-samtools-1.3.1_GH0.tar.gz) = 3757176
+TIMESTAMP = 1508304738
+SHA256 (samtools-samtools-1.6_GH0.tar.gz) = c0d1ffefe441297ee0eec0e032ac3131519f82fd1a11d38fbcec19e2d5822b28
+SIZE (samtools-samtools-1.6_GH0.tar.gz) = 4014195
Modified: head/biology/samtools/files/patch-Makefile
==============================================================================
--- head/biology/samtools/files/patch-Makefile Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/samtools/files/patch-Makefile Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,11 +1,11 @@
---- Makefile.orig 2016-04-22 09:22:44 UTC
+--- Makefile.orig 2017-09-28 11:12:01 UTC
+++ Makefile
-@@ -38,18 +38,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_
+@@ -40,23 +40,22 @@ AOBJS= bam_index.o bam_plcmd.o sam_
bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
- bam_quickcheck.o bam_addrprg.o
+ bam_quickcheck.o bam_addrprg.o bam_markdup.o
-prefix = /usr/local
-+prefix = ${STAGEDIR}${PREFIX}
++prefix = ${PREFIX}
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
datarootdir = $(prefix)/share
@@ -13,46 +13,22 @@
+mandir = $(prefix)/man
man1dir = $(mandir)/man1
--MKDIR_P = mkdir -p
+ # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
+-misc_bindir = $(bindir)
++misc_bindir = $(bindir)/samtools_misc
+
+ MKDIR_P = mkdir -p
-INSTALL = install -p
--INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
-+#MKDIR_P = mkdir -p
-+#INSTALL = install -p
-+#INSTALL_PROGRAM = $(INSTALL)
-+#INSTALL_DATA = $(INSTALL) -m 644
-+#INSTALL_DIR = $(MKDIR_P) -m 755
+-INSTALL_MAN = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
++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 = samtools
-@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \
- misc/md5fa misc/md5sum-lite misc/wgsim
-
- MISC_PROGRAMS = \
-- $(BUILT_MISC_PROGRAMS) \
- misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
- misc/interpolate_sam.pl misc/novo2sam.pl \
- misc/plot-bamstats misc/psl2sam.pl \
-@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
- # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
- ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
- ALL_LDFLAGS = -rdynamic $(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.
-@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf
-
-
- install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
-- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
-- $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
-+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
-+ $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
-+ $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
-+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
- $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
-
-
Modified: head/biology/samtools/files/patch-test_test.pl
==============================================================================
--- head/biology/samtools/files/patch-test_test.pl Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/samtools/files/patch-test_test.pl Wed Oct 25 10:19:50 2017 (r452840)
@@ -1,15 +1,6 @@
---- test/test.pl.orig 2015-12-22 22:43:15 UTC
+--- test/test.pl.orig 2017-10-18 06:08:39 UTC
+++ test/test.pl
-@@ -136,7 +136,7 @@ sub _cmd
- else
- {
- # child
-- exec('/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/bin/sh -o pipefail -c $cmd]: $!");
-+ exec('/usr/local/bin/bash', '-o','pipefail','-c', "($cmd) 2> $err_filename") or error("Cannot execute the command [/usr/local/bin/bash -o pipefail -c $cmd]: $!");
- }
- }
- sub cmd
-@@ -560,7 +560,7 @@ sub test_usage
+@@ -636,7 +636,7 @@ sub test_usage
my $command = $args{cmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
@@ -18,7 +9,7 @@
my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
-@@ -615,7 +615,7 @@ sub test_usage_subcommand
+@@ -694,7 +694,7 @@ sub test_usage_subcommand
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
Modified: head/biology/samtools/files/pkg-message.in
==============================================================================
--- head/biology/samtools/files/pkg-message.in Wed Oct 25 10:12:26 2017 (r452839)
+++ head/biology/samtools/files/pkg-message.in Wed Oct 25 10:19:50 2017 (r452840)
@@ -3,5 +3,5 @@ The miscellaneous tools included with Samtools have be
Add that directory to your path if you want to use these tools.
-Some of these tools depend on Perl5, and it will need to be installed to
+Some of these tools depend on Perl5/Python, and it will need to be installed to
use them.
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