From owner-svn-ports-head@freebsd.org Wed Oct 25 10:19:53 2017 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 8E471E45651; Wed, 25 Oct 2017 10:19:53 +0000 (UTC) (envelope-from pizzamig@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 56D6A6623D; Wed, 25 Oct 2017 10:19:53 +0000 (UTC) (envelope-from pizzamig@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id v9PAJqmJ086790; Wed, 25 Oct 2017 10:19:52 GMT (envelope-from pizzamig@FreeBSD.org) Received: (from pizzamig@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id v9PAJolt086771; Wed, 25 Oct 2017 10:19:50 GMT (envelope-from pizzamig@FreeBSD.org) Message-Id: <201710251019.v9PAJolt086771@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: pizzamig set sender to pizzamig@FreeBSD.org using -f From: Luca Pizzamiglio Date: Wed, 25 Oct 2017 10:19:50 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r452840 - in head/biology: bcftools bcftools/files htslib htslib/files samtools samtools/files X-SVN-Group: ports-head X-SVN-Commit-Author: pizzamig X-SVN-Commit-Paths: in head/biology: bcftools bcftools/files htslib htslib/files samtools samtools/files X-SVN-Commit-Revision: 452840 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 25 Oct 2017 10:19:53 -0000 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@niid.go.jp Approved by: cartwright@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@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 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@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}) && !$args{exit_on_error} ) { return @out; } Modified: head/biology/bcftools/files/patch-prob1.c ============================================================================== --- head/biology/bcftools/files/patch-prob1.c Wed Oct 25 10:12:26 2017 (r452839) +++ head/biology/bcftools/files/patch-prob1.c Wed Oct 25 10:19:50 2017 (r452840) @@ -1,4 +1,4 @@ ---- prob1.c.orig 2015-12-15 21:42:34 UTC +--- prob1.c.orig 2017-09-28 11:22:48 UTC +++ prob1.c @@ -33,6 +33,12 @@ THE SOFTWARE. */ #include Modified: head/biology/bcftools/files/patch-test_test.pl ============================================================================== --- head/biology/bcftools/files/patch-test_test.pl Wed Oct 25 10:12:26 2017 (r452839) +++ head/biology/bcftools/files/patch-test_test.pl Wed Oct 25 10:19:50 2017 (r452840) @@ -1,6 +1,6 @@ ---- test/test.pl.orig 2015-12-22 22:45:13 UTC +--- test/test.pl.orig 2017-10-18 09:33:24 UTC +++ test/test.pl -@@ -290,7 +290,7 @@ sub _cmd +@@ -381,7 +381,7 @@ sub _cmd else { # child @@ -9,7 +9,7 @@ } return ($? >> 8, join('',@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@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 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 - +#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@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 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.