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biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

Browse Source 
- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)
This commit is contained in:
Jason Unovitch 2015-12-25 01:31:09 +00:00
parent 19dd31f478
commit d5dffd3623
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=404398
27 changed files with 930 additions and 173 deletions
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20
biology/bcftools/Makefile
View File

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= bcftools
PORTVERSION= 1.2
PORTVERSION= 1.3
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu
@ -11,15 +11,17 @@ COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= htslib>=1.2:${PORTSDIR}/biology/htslib
BUILD_DEPENDS= htslib>=1.3:${PORTSDIR}/biology/htslib
LIB_DEPENDS= libhts.so:${PORTSDIR}/biology/htslib
TEST_DEPENDS= bash:${PORTSDIR}/shells/bash
USE_GITHUB= yes
GH_ACCOUNT= samtools
USES= gmake shebangfix
USES= gmake perl5 shebangfix
USE_PERL5= test
SUB_FILES= pkg-message
SHEBANG_FILES= vcfutils.pl
SHEBANG_FILES= vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl
OPTIONS_DEFINE= GPL
GPL_DESC= Enable modules that rely on GPL code
@ -33,10 +35,10 @@ CPPFLAGS+= -I${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}"
INSTALL_DATA="${INSTALL_DATA}" \
INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
INSTALL_DIR="${MKDIR}"
.if ${PORT_OPTIONS:MGPL}
MAKE_ENV+= USE_GPL=1
@ -45,4 +47,6 @@ LICENSE= GPLv3
PLIST_SUB= PORTVERSION="${PORTVERSION}"
TEST_TARGET= test
.include <bsd.port.mk>

4
biology/bcftools/distinfo
View File

@ -1,2 +1,2 @@
SHA256 (samtools-bcftools-1.2_GH0.tar.gz) = 90ccd7dccfb0b2848b71f32fff073c420260e857b7feeb89c1fb4bfaba49bfba
SIZE (samtools-bcftools-1.2_GH0.tar.gz) = 511625
SHA256 (samtools-bcftools-1.3_GH0.tar.gz) = 3f4d4bf68637070cb7dbb5d5619ece7e3315727e651eab751d849085439b11d8
SIZE (samtools-bcftools-1.3_GH0.tar.gz) = 943041

86
biology/bcftools/files/patch-Makefile
View File

@ -1,84 +1,78 @@
--- Makefile.orig 2015-02-02 15:40:17 UTC
--- Makefile.orig 2015-12-15 21:42:34 UTC
+++ Makefile
@@ -29,14 +29,13 @@ TEST_PROG= test/test-rbuf
@@ -29,16 +29,15 @@ TEST_PROG= test/test-rbuf
all: $(PROG) $(TEST_PROG)
# 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)/bgzip
TABIX = $(HTSDIR)/tabix
+BGZIP = $(HTSDIR)/../bin/bgzip
+TABIX = $(HTSDIR)/../bin/tabix
-CC = gcc
-CPPFLAGS =
-CFLAGS = -g -Wall -Wc++-compat -O2
+CC ?= cc
+CFLAGS += -Wall
DFLAGS =
-LDFLAGS =
+CC ?= cc
+CPPFLAGS +=
+CFLAGS += -Wall
+LDFLAGS +=
LIBS =
OBJS = main.o vcfindex.o tabix.o \
vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
@@ -52,22 +51,15 @@ INCLUDES = -I. -I$(HTSDIR)
@@ -57,26 +56,20 @@ GSL_LIBS =
ifdef USE_GPL
CFLAGS += -DUSE_GPL
OBJS += polysomy.o
- LDLIBS = -lgsl -lcblas
+ LDLIBS += -lgsl -lgslcblas
EXTRA_CPPFLAGS += -DUSE_GPL
OBJS += polysomy.o peakfit.o
- GSL_LIBS = -lgsl -lcblas
+ GSL_LIBS = -lgsl -lgslcblas
endif
-prefix = /usr/local
+prefix = ${STAGEDIR}${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
plugindir = $(libexecdir)/bcftools
pluginpath = $(plugindir)
-MKDIR_P = mkdir -p
-INSTALL = install -p
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
-
-
MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
all:$(PROG) plugins
@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o
$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
# See htslib/Makefile
@@ -102,8 +94,8 @@ PLUGINC = $(foreach dir, plugins, $(wild
PLUGINS = $(PLUGINC:.c=.so)
PLUGINM = $(PLUGINC:.c=.mk)
-%.so: %.c version.h version.c $(HTSDIR)/libhts.so
- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -L$(HTSDIR) -lhts
+%.so: %.c version.h version.c
+ $(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ version.c $< -lhts
-include $(PLUGINM)
@@ -156,10 +148,10 @@ version.o: version.h version.c
test/test-rbuf.o: test/test-rbuf.c rbuf.h
test/test-rbuf: test/test-rbuf.o
- $(CC) $(CFLAGS) -o $@ -lm -ldl $<
+ $(CC) $(CFLAGS) -o $@ -lm $<
-bcftools: $(HTSLIB) $(OBJS)
- $(CC) $(CFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(LDLIBS)
+bcftools: $(OBJS)
+ $(CC) -pthread $(CFLAGS) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lz -lm $(LDLIBS)
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) $(LIBS)
doc/bcftools.1: doc/bcftools.txt
cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
@@ -170,8 +162,9 @@ doc/bcftools.html: doc/bcftools.txt
docs: doc/bcftools.1 doc/bcftools.html
install: $(PROG) doc/bcftools.1
- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
- $(INSTALL_PROGRAM) $(PROG) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)
+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
@@ -198,8 +191,9 @@ 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_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) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)/samtools_misc
+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
clean: testclean clean-plugins

7
biology/bcftools/files/patch-plugins_fixploidy.mk
View File

@ -1,7 +0,0 @@
--- plugins/fixploidy.mk.orig 2015-02-02 15:40:17 UTC
+++ plugins/fixploidy.mk
@@ -1,2 +1,2 @@
-plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
+plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
+ $(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts

7
biology/bcftools/files/patch-plugins_vcf2sex.mk
View File

@ -1,7 +0,0 @@
--- plugins/vcf2sex.mk.orig 2015-02-02 15:40:17 UTC
+++ plugins/vcf2sex.mk
@@ -1,2 +1,2 @@
-plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
- $(CC) $(CFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -L$(HTSDIR) -lhts
+plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
+ $(CC) $(CFLAGS) $(LDFLAGS) $(INCLUDES) -fPIC -shared -o $@ ploidy.c version.c $< -lhts

12
biology/bcftools/files/patch-prob1.c
View File

@ -1,15 +1,13 @@
--- prob1.c.orig 2015-04-28 01:28:23 UTC
--- prob1.c.orig 2015-12-15 21:42:34 UTC
+++ prob1.c
@@ -33,6 +33,14 @@ THE SOFTWARE. */
@@ -33,6 +33,12 @@ THE SOFTWARE. */
#include <zlib.h>
#include "prob1.h"
+#include <sys/param.h>
+#ifdef __FreeBSD__
+# if __FreeBSD_version < 1000034
+# define logl(x) log(x)
+# define expl(x) exp(x)
+# endif
+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
+# define logl(x) log(x)
+# define expl(x) exp(x)
+#endif
+
// #include "kstring.h"

29
biology/bcftools/files/patch-test_test.pl Normal file
View File

@ -0,0 +1,29 @@
--- test/test.pl.orig 2015-12-22 22:45:13 UTC
+++ test/test.pl
@@ -290,7 +290,7 @@ 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]: $!");
}
return ($? >> 8, join('',@out));
}
@@ -657,7 +657,7 @@ sub test_usage
my $command = $args{cmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
- if ( $out =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
+ if ( $out =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,$test,"could not run $commandpath: $out"); return; }
my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
@@ -708,7 +708,7 @@ sub test_usage_subcommand
my $subcommand = $args{subcmd};
my $commandpath = $$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: $out"); return; }
my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);

7
biology/bcftools/files/pkg-message.in
View File

@ -1,2 +1,7 @@
The miscellaneous tools included with Bcftools have been installed to
%%PREFIX%%/bin/samtools_misc
Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
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
use them.

14
biology/bcftools/pkg-plist
View File

@ -1,4 +1,18 @@
bin/bcftools
bin/samtools_misc/color-chrs.pl
bin/samtools_misc/plot-vcfstats
bin/samtools_misc/vcfutils.pl
libexec/bcftools/color-chrs.so
libexec/bcftools/counts.so
libexec/bcftools/dosage.so
libexec/bcftools/fill-AN-AC.so
libexec/bcftools/fill-tags.so
libexec/bcftools/fixploidy.so
libexec/bcftools/frameshifts.so
libexec/bcftools/impute-info.so
libexec/bcftools/mendelian.so
libexec/bcftools/missing2ref.so
libexec/bcftools/setGT.so
libexec/bcftools/tag2tag.so
libexec/bcftools/vcf2sex.so
man/man1/bcftools.1.gz

23
biology/htslib/Makefile
View File

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= htslib
PORTVERSION= 1.2.1
PORTVERSION= 1.3
CATEGORIES= biology devel
MAINTAINER= cartwright@asu.edu
@ -12,13 +12,26 @@ LICENSE= BSD3CLAUSE MIT
LICENSE_COMB= multi
LICENSE_FILE= ${WRKSRC}/LICENSE
TEST_DEPENDS= bash:${PORTSDIR}/shells/bash
USE_GITHUB= yes
GH_ACCOUNT= samtools
USES= gmake
USES= autoreconf gmake perl5 shebangfix
USE_PERL5= test
USE_LDCONFIG= yes
USE_AUTOTOOLS= autoconf
GNU_CONFIGURE=yes
GNU_CONFIGURE= yes
SHEBANG_FILES= test/compare_sam.pl test/test.pl test/test_view.pl
OPTIONS_DEFINE= CURL
OPTIONS_DEFAULT= CURL
CURL_DESC= Use libcurl for network file access (HTTPS and S3 support).
CURL_LIB_DEPENDS= libcurl.so:${PORTSDIR}/ftp/curl
CURL_CONFIGURE_ENABLE= libcurl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
INSTALL_DATA="${INSTALL_DATA}" \
@ -27,6 +40,8 @@ MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
PLIST_SUB= PORTVERSION="${PORTVERSION}"
TEST_TARGET= test
post-patch:
@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' ${WRKSRC}/configure.ac

4
biology/htslib/distinfo
View File

@ -1,2 +1,2 @@
SHA256 (samtools-htslib-1.2.1_GH0.tar.gz) = 4f67f0fc73ae86f3ed4336d8d8f6da3c12066e9cb5f142b685622dd6b8f9ae42
SIZE (samtools-htslib-1.2.1_GH0.tar.gz) = 997625
SHA256 (samtools-htslib-1.3_GH0.tar.gz) = 291a54090df3bc367b509890e1cfa34d53b1ee9be42c5fa6c2b1e2ec8f8b13af
SIZE (samtools-htslib-1.3_GH0.tar.gz) = 1042953

27
biology/htslib/files/patch-Makefile
View File

@ -1,6 +1,6 @@
--- Makefile.orig 2015-02-03 16:22:23 UTC
--- Makefile.orig 2015-12-15 16:34:33 UTC
+++ Makefile
@@ -22,16 +22,9 @@
@@ -22,16 +22,7 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
@ -8,19 +8,18 @@
-AR = ar
-RANLIB = ranlib
-
-CPPFLAGS = -I.
+CPPFLAGS += -I.
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
-CPPFLAGS =
-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
-CFLAGS = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
-LDFLAGS =
-LDLIBS =
-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.
@@ -57,16 +50,10 @@ bindir = $(exec_prefix)/bin
includedir = $(prefix)/include
@@ -58,16 +49,10 @@ includedir = $(prefix)/include
libdir = $(exec_prefix)/lib
libexecdir = $(exec_prefix)/libexec
datarootdir = $(prefix)/share
-mandir = $(datarootdir)/man
+mandir = $(prefix)/man
@ -35,18 +34,18 @@
-INSTALL_DIR = $(MKDIR_P) -m 755
+pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
BUILT_PROGRAMS = \
bgzip \
@@ -82,7 +69,7 @@ BUILT_TEST_PROGRAMS = \
# Set by config.mk if plugins are enabled
plugindir =
@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
test/test-vcf-api \
test/test-vcf-sweep
-all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
+all: lib-static lib-shared $(BUILT_PROGRAMS)
-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
+all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
HTSPREFIX =
include htslib_vars.mk
@@ -332,7 +319,7 @@ installdirs:
@@ -361,7 +346,7 @@ installdirs:
# and libhts.so.NN (used by client executables at runtime).
install-so: libhts.so installdirs

4
biology/htslib/files/patch-configure.ac
View File

@ -1,11 +1,11 @@
--- configure.ac.orig 2015-02-03 16:22:23 UTC
--- configure.ac.orig 2015-12-15 16:34:33 UTC
+++ configure.ac
@@ -23,7 +23,7 @@
# DEALINGS IN THE SOFTWARE.
dnl Process this file with autoconf to produce a configure script
-AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
+AC_INIT([HTSlib], [@PORTVERSION@],
+AC_INIT([HTSlib], [1.3],
[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(hts.c)

10
biology/htslib/files/patch-cram_cram__io.c
View File

@ -1,10 +0,0 @@
--- cram/cram_io.c.orig 2015-02-03 16:22:23 UTC
+++ cram/cram_io.c
@@ -53,6 +53,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE
#include <assert.h>
#include <stdlib.h>
#include <string.h>
+#include <unistd.h>
#include <zlib.h>
#ifdef HAVE_LIBBZ2
#include <bzlib.h>

14
biology/htslib/files/patch-hfile__libcurl.c Normal file
View File

@ -0,0 +1,14 @@
--- hfile_libcurl.c.orig 2015-12-22 22:35:42 UTC
+++ hfile_libcurl.c
@@ -39,6 +39,11 @@ DEALINGS IN THE SOFTWARE. */
#include <curl/curl.h>
+#include <sys/param.h>
+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000033) && !defined(ENOTRECOVERABLE)
+# define ENOTRECOVERABLE EIO
+#endif
+
typedef struct {
hFILE base;
CURL *easy;

2
biology/htslib/pkg-plist
View File

@ -2,10 +2,12 @@ bin/bgzip
bin/htsfile
bin/tabix
include/htslib/bgzf.h
include/htslib/cram.h
include/htslib/faidx.h
include/htslib/hfile.h
include/htslib/hts.h
include/htslib/hts_defs.h
include/htslib/kbitset.h
include/htslib/kfunc.h
include/htslib/khash.h
include/htslib/khash_str2int.h

17
biology/samtools/Makefile
View File

@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= samtools
PORTVERSION= 1.2
PORTVERSION= 1.3
CATEGORIES= biology
MAINTAINER= cartwright@asu.edu
@ -11,13 +11,17 @@ COMMENT= Tools for manipulating next-generation sequencing data
LICENSE= MIT
LICENSE_FILE= ${WRKSRC}/LICENSE
BUILD_DEPENDS= htslib>=1.2:${PORTSDIR}/biology/htslib
BUILD_DEPENDS= htslib>=1.3:${PORTSDIR}/biology/htslib
LIB_DEPENDS= libhts.so:${PORTSDIR}/biology/htslib
TEST_DEPENDS= bash:${PORTSDIR}/shells/bash
USE_GITHUB= yes
USES= gmake
USES= autoreconf gmake perl5 shebangfix
USE_PERL5= test
GNU_CONFIGURE= yes
SUB_FILES= pkg-message
SHEBANG_FILES= misc/*.pl misc/plot-bamstats test/test.pl
CPPFLAGS+= -I${LOCALBASE}/include
LDFLAGS+= -L${LOCALBASE}/lib
@ -30,4 +34,11 @@ MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
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>

4
biology/samtools/distinfo
View File

@ -1,2 +1,2 @@
SHA256 (samtools-samtools-1.2_GH0.tar.gz) = e4be60ad24fe0324b9384fe58ec2ab7359fe926fbee3115d869c447eb01a9e47
SIZE (samtools-samtools-1.2_GH0.tar.gz) = 4318615
SHA256 (samtools-samtools-1.3_GH0.tar.gz) = f1eee9a217d547d9b483098519738ef351ec454f4a85cdb1e77ae8892fe858b5
SIZE (samtools-samtools-1.3_GH0.tar.gz) = 3742904

518
biology/samtools/files/ax_with_curses.m4 Normal file
View File

@ -0,0 +1,518 @@
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_with_curses.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_WITH_CURSES
#
# DESCRIPTION
#
# This macro checks whether a SysV or X/Open-compatible Curses library is
# present, along with the associated header file. The NcursesW
# (wide-character) library is searched for first, followed by Ncurses,
# then the system-default plain Curses. The first library found is the
# one returned.
#
# The following options are understood: --with-ncursesw, --with-ncurses,
# --without-ncursesw, --without-ncurses. The "--with" options force the
# macro to use that particular library, terminating with an error if not
# found. The "--without" options simply skip the check for that library.
# The effect on the search pattern is:
#
# (no options) - NcursesW, Ncurses, Curses
# --with-ncurses --with-ncursesw - NcursesW only [*]
# --without-ncurses --with-ncursesw - NcursesW only [*]
# --with-ncursesw - NcursesW only [*]
# --with-ncurses --without-ncursesw - Ncurses only [*]
# --with-ncurses - NcursesW, Ncurses [**]
# --without-ncurses --without-ncursesw - Curses only
# --without-ncursesw - Ncurses, Curses
# --without-ncurses - NcursesW, Curses
#
# [*] If the library is not found, abort the configure script.
#
# [**] If the second library (Ncurses) is not found, abort configure.
#
# The following preprocessor symbols may be defined by this macro if the
# appropriate conditions are met:
#
# HAVE_CURSES - if any SysV or X/Open Curses library found
# HAVE_CURSES_ENHANCED - if library supports X/Open Enhanced functions
# HAVE_CURSES_COLOR - if library supports color (enhanced functions)
# HAVE_CURSES_OBSOLETE - if library supports certain obsolete features
# HAVE_NCURSESW - if NcursesW (wide char) library is to be used
# HAVE_NCURSES - if the Ncurses library is to be used
#
# HAVE_CURSES_H - if <curses.h> is present and should be used
# HAVE_NCURSESW_H - if <ncursesw.h> should be used
# HAVE_NCURSES_H - if <ncurses.h> should be used
# HAVE_NCURSESW_CURSES_H - if <ncursesw/curses.h> should be used
# HAVE_NCURSES_CURSES_H - if <ncurses/curses.h> should be used
#
# (These preprocessor symbols are discussed later in this document.)
#
# The following output variable is defined by this macro; it is precious
# and may be overridden on the ./configure command line:
#
# CURSES_LIB - library to add to xxx_LDADD
#
# The library listed in CURSES_LIB is NOT added to LIBS by default. You
# need to add CURSES_LIB to the appropriate xxx_LDADD line in your
# Makefile.am. For example:
#
# prog_LDADD = @CURSES_LIB@
#
# If CURSES_LIB is set on the configure command line (such as by running
# "./configure CURSES_LIB=-lmycurses"), then the only header searched for
# is <curses.h>. The user may use the CPPFLAGS precious variable to
# override the standard #include search path. If the user needs to
# specify an alternative path for a library (such as for a non-standard
# NcurseW), the user should use the LDFLAGS variable.
#
# The following shell variables may be defined by this macro:
#
# ax_cv_curses - set to "yes" if any Curses library found
# ax_cv_curses_enhanced - set to "yes" if Enhanced functions present
# ax_cv_curses_color - set to "yes" if color functions present
# ax_cv_curses_obsolete - set to "yes" if obsolete features present
#
# ax_cv_ncursesw - set to "yes" if NcursesW library found
# ax_cv_ncurses - set to "yes" if Ncurses library found
# ax_cv_plaincurses - set to "yes" if plain Curses library found
# ax_cv_curses_which - set to "ncursesw", "ncurses", "plaincurses" or "no"
#
# These variables can be used in your configure.ac to determine the level
# of support you need from the Curses library. For example, if you must
# have either Ncurses or NcursesW, you could include:
#
# AX_WITH_CURSES
# if test "x$ax_cv_ncursesw" != xyes && test "x$ax_cv_ncurses" != xyes; then
# AC_MSG_ERROR([requires either NcursesW or Ncurses library])
# fi
#
# If any Curses library will do (but one must be present and must support
# color), you could use:
#
# AX_WITH_CURSES
# if test "x$ax_cv_curses" != xyes || test "x$ax_cv_curses_color" != xyes; then
# AC_MSG_ERROR([requires an X/Open-compatible Curses library with color])
# fi
#
# Certain preprocessor symbols and shell variables defined by this macro
# can be used to determine various features of the Curses library. In
# particular, HAVE_CURSES and ax_cv_curses are defined if the Curses
# library found conforms to the traditional SysV and/or X/Open Base Curses
# definition. Any working Curses library conforms to this level.
#
# HAVE_CURSES_ENHANCED and ax_cv_curses_enhanced are defined if the
# library supports the X/Open Enhanced Curses definition. In particular,
# the wide-character types attr_t, cchar_t and wint_t, the functions
# wattr_set() and wget_wch() and the macros WA_NORMAL and _XOPEN_CURSES
# are checked. The Ncurses library does NOT conform to this definition,
# although NcursesW does.
#
# HAVE_CURSES_COLOR and ax_cv_curses_color are defined if the library
# supports color functions and macros such as COLOR_PAIR, A_COLOR,
# COLOR_WHITE, COLOR_RED and init_pair(). These are NOT part of the
# X/Open Base Curses definition, but are part of the Enhanced set of
# functions. The Ncurses library DOES support these functions, as does
# NcursesW.
#
# HAVE_CURSES_OBSOLETE and ax_cv_curses_obsolete are defined if the
# library supports certain features present in SysV and BSD Curses but not
# defined in the X/Open definition. In particular, the functions
# getattrs(), getcurx() and getmaxx() are checked.
#
# To use the HAVE_xxx_H preprocessor symbols, insert the following into
# your system.h (or equivalent) header file:
#
# #if defined HAVE_NCURSESW_CURSES_H
# # include <ncursesw/curses.h>
# #elif defined HAVE_NCURSESW_H
# # include <ncursesw.h>
# #elif defined HAVE_NCURSES_CURSES_H
# # include <ncurses/curses.h>
# #elif defined HAVE_NCURSES_H
# # include <ncurses.h>
# #elif defined HAVE_CURSES_H
# # include <curses.h>
# #else
# # error "SysV or X/Open-compatible Curses header file required"
# #endif
#
# For previous users of this macro: you should not need to change anything
# in your configure.ac or Makefile.am, as the previous (serial 10)
# semantics are still valid. However, you should update your system.h (or
# equivalent) header file to the fragment shown above. You are encouraged
# also to make use of the extended functionality provided by this version
# of AX_WITH_CURSES, as well as in the additional macros
# AX_WITH_CURSES_PANEL, AX_WITH_CURSES_MENU and AX_WITH_CURSES_FORM.
#
# LICENSE
#
# Copyright (c) 2009 Mark Pulford <mark@kyne.com.au>
# Copyright (c) 2009 Damian Pietras <daper@daper.net>
# Copyright (c) 2012 Reuben Thomas <rrt@sc3d.org>
# Copyright (c) 2011 John Zaitseff <J.Zaitseff@zap.org.au>
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.
#
# As a special exception, the respective Autoconf Macro's copyright owner
# gives unlimited permission to copy, distribute and modify the configure
# scripts that are the output of Autoconf when processing the Macro. You
# need not follow the terms of the GNU General Public License when using
# or distributing such scripts, even though portions of the text of the
# Macro appear in them. The GNU General Public License (GPL) does govern
# all other use of the material that constitutes the Autoconf Macro.
#
# This special exception to the GPL applies to versions of the Autoconf
# Macro released by the Autoconf Archive. When you make and distribute a
# modified version of the Autoconf Macro, you may extend this special
# exception to the GPL to apply to your modified version as well.
#serial 15
AU_ALIAS([MP_WITH_CURSES], [AX_WITH_CURSES])
AC_DEFUN([AX_WITH_CURSES], [
AC_ARG_VAR([CURSES_LIB], [linker library for Curses, e.g. -lcurses])
AC_ARG_WITH([ncurses], [AS_HELP_STRING([--with-ncurses],
[force the use of Ncurses or NcursesW])],
[], [with_ncurses=check])
AC_ARG_WITH([ncursesw], [AS_HELP_STRING([--without-ncursesw],
[do not use NcursesW (wide character support)])],
[], [with_ncursesw=check])
ax_saved_LIBS=$LIBS
AS_IF([test "x$with_ncurses" = xyes || test "x$with_ncursesw" = xyes],
[ax_with_plaincurses=no], [ax_with_plaincurses=check])
ax_cv_curses_which=no
# Test for NcursesW
AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncursesw" != xno], [
LIBS="$ax_saved_LIBS -lncursesw"
AC_CACHE_CHECK([for NcursesW wide-character library], [ax_cv_ncursesw], [
AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
[ax_cv_ncursesw=yes], [ax_cv_ncursesw=no])
])
AS_IF([test "x$ax_cv_ncursesw" = xno && test "x$with_ncursesw" = xyes], [
AC_MSG_ERROR([--with-ncursesw specified but could not find NcursesW library])
])
AS_IF([test "x$ax_cv_ncursesw" = xyes], [
ax_cv_curses=yes
ax_cv_curses_which=ncursesw
CURSES_LIB="-lncursesw"
AC_DEFINE([HAVE_NCURSESW], [1], [Define to 1 if the NcursesW library is present])
AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
AC_CACHE_CHECK([for working ncursesw/curses.h], [ax_cv_header_ncursesw_curses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <ncursesw/curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_header_ncursesw_curses_h=yes],
[ax_cv_header_ncursesw_curses_h=no])
])
AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSESW_CURSES_H], [1], [Define to 1 if <ncursesw/curses.h> is present])
])
AC_CACHE_CHECK([for working ncursesw.h], [ax_cv_header_ncursesw_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <ncursesw.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_header_ncursesw_h=yes],
[ax_cv_header_ncursesw_h=no])
])
AS_IF([test "x$ax_cv_header_ncursesw_h" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSESW_H], [1], [Define to 1 if <ncursesw.h> is present])
])
AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h_with_ncursesw], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <ncurses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_header_ncurses_h_with_ncursesw=yes],
[ax_cv_header_ncurses_h_with_ncursesw=no])
])
AS_IF([test "x$ax_cv_header_ncurses_h_with_ncursesw" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
])
AS_IF([test "x$ax_cv_header_ncursesw_curses_h" = xno && test "x$ax_cv_header_ncursesw_h" = xno && test "x$ax_cv_header_ncurses_h_with_ncursesw" = xno], [
AC_MSG_WARN([could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h])
])
])
])
# Test for Ncurses
AS_IF([test "x$CURSES_LIB" = x && test "x$with_ncurses" != xno && test "x$ax_cv_curses_which" = xno], [
LIBS="$ax_saved_LIBS -lncurses"
AC_CACHE_CHECK([for Ncurses library], [ax_cv_ncurses], [
AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
[ax_cv_ncurses=yes], [ax_cv_ncurses=no])
])
AS_IF([test "x$ax_cv_ncurses" = xno && test "x$with_ncurses" = xyes], [
AC_MSG_ERROR([--with-ncurses specified but could not find Ncurses library])
])
AS_IF([test "x$ax_cv_ncurses" = xyes], [
ax_cv_curses=yes
ax_cv_curses_which=ncurses
CURSES_LIB="-lncurses"
AC_DEFINE([HAVE_NCURSES], [1], [Define to 1 if the Ncurses library is present])
AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
AC_CACHE_CHECK([for working ncurses/curses.h], [ax_cv_header_ncurses_curses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <ncurses/curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
]])],
[ax_cv_header_ncurses_curses_h=yes],
[ax_cv_header_ncurses_curses_h=no])
])
AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xyes], [
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSES_CURSES_H], [1], [Define to 1 if <ncurses/curses.h> is present])
])
AC_CACHE_CHECK([for working ncurses.h], [ax_cv_header_ncurses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <ncurses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
]])],
[ax_cv_header_ncurses_h=yes],
[ax_cv_header_ncurses_h=no])
])
AS_IF([test "x$ax_cv_header_ncurses_h" = xyes], [
ax_cv_curses_color=yes
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
AC_DEFINE([HAVE_NCURSES_H], [1], [Define to 1 if <ncurses.h> is present])
])
AS_IF([test "x$ax_cv_header_ncurses_curses_h" = xno && test "x$ax_cv_header_ncurses_h" = xno], [
AC_MSG_WARN([could not find a working ncurses/curses.h or ncurses.h])
])
])
])
# Test for plain Curses (or if CURSES_LIB was set by user)
AS_IF([test "x$with_plaincurses" != xno && test "x$ax_cv_curses_which" = xno], [
AS_IF([test "x$CURSES_LIB" != x], [
LIBS="$ax_saved_LIBS $CURSES_LIB"
], [
LIBS="$ax_saved_LIBS -lcurses"
])
AC_CACHE_CHECK([for Curses library], [ax_cv_plaincurses], [
AC_LINK_IFELSE([AC_LANG_CALL([], [initscr])],
[ax_cv_plaincurses=yes], [ax_cv_plaincurses=no])
])
AS_IF([test "x$ax_cv_plaincurses" = xyes], [
ax_cv_curses=yes
ax_cv_curses_which=plaincurses
AS_IF([test "x$CURSES_LIB" = x], [
CURSES_LIB="-lcurses"
])
AC_DEFINE([HAVE_CURSES], [1], [Define to 1 if a SysV or X/Open compatible Curses library is present])
# Check for base conformance (and header file)
AC_CACHE_CHECK([for working curses.h], [ax_cv_header_curses_h], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
initscr();
]])],
[ax_cv_header_curses_h=yes],
[ax_cv_header_curses_h=no])
])
AS_IF([test "x$ax_cv_header_curses_h" = xyes], [
AC_DEFINE([HAVE_CURSES_H], [1], [Define to 1 if <curses.h> is present])
# Check for X/Open Enhanced conformance
AC_CACHE_CHECK([for X/Open Enhanced Curses conformance], [ax_cv_plaincurses_enhanced], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <curses.h>
@%:@ifndef _XOPEN_CURSES
@%:@error "this Curses library is not enhanced"
"this Curses library is not enhanced"
@%:@endif
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
attr_t d = WA_NORMAL;
cchar_t e;
wint_t f;
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
wattr_set(stdscr, d, 0, NULL);
wget_wch(stdscr, &f);
]])],
[ax_cv_plaincurses_enhanced=yes],
[ax_cv_plaincurses_enhanced=no])
])
AS_IF([test "x$ax_cv_plaincurses_enhanced" = xyes], [
ax_cv_curses_enhanced=yes
ax_cv_curses_color=yes
AC_DEFINE([HAVE_CURSES_ENHANCED], [1], [Define to 1 if library supports X/Open Enhanced functions])
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
])
# Check for color functions
AC_CACHE_CHECK([for Curses color functions], [ax_cv_plaincurses_color], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@define _XOPEN_SOURCE_EXTENDED 1
@%:@include <curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
chtype c = COLOR_PAIR(1) & A_COLOR;
initscr();
init_pair(1, COLOR_WHITE, COLOR_RED);
]])],
[ax_cv_plaincurses_color=yes],
[ax_cv_plaincurses_color=no])
])
AS_IF([test "x$ax_cv_plaincurses_color" = xyes], [
ax_cv_curses_color=yes
AC_DEFINE([HAVE_CURSES_COLOR], [1], [Define to 1 if library supports color (enhanced functions)])
])
# Check for obsolete functions
AC_CACHE_CHECK([for obsolete Curses functions], [ax_cv_plaincurses_obsolete], [
AC_LINK_IFELSE([AC_LANG_PROGRAM([[
@%:@include <curses.h>
]], [[
chtype a = A_BOLD;
int b = KEY_LEFT;
int g = getattrs(stdscr);
int h = getcurx(stdscr) + getmaxx(stdscr);
initscr();
]])],
[ax_cv_plaincurses_obsolete=yes],
[ax_cv_plaincurses_obsolete=no])
])
AS_IF([test "x$ax_cv_plaincurses_obsolete" = xyes], [
ax_cv_curses_obsolete=yes
AC_DEFINE([HAVE_CURSES_OBSOLETE], [1], [Define to 1 if library supports certain obsolete features])
])
])
AS_IF([test "x$ax_cv_header_curses_h" = xno], [
AC_MSG_WARN([could not find a working curses.h])
])
])
])
AS_IF([test "x$ax_cv_curses" != xyes], [ax_cv_curses=no])
AS_IF([test "x$ax_cv_curses_enhanced" != xyes], [ax_cv_curses_enhanced=no])
AS_IF([test "x$ax_cv_curses_color" != xyes], [ax_cv_curses_color=no])
AS_IF([test "x$ax_cv_curses_obsolete" != xyes], [ax_cv_curses_obsolete=no])
LIBS=$ax_saved_LIBS
])dnl

140
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@ -0,0 +1,140 @@
# ===========================================================================
# http://www.gnu.org/software/autoconf-archive/ax_with_htslib.html
# ===========================================================================
#
# SYNOPSIS
#
# AX_WITH_HTSLIB
#
# DESCRIPTION
#
# This macro checks whether HTSlib <http://www.htslib.org/> is installed
# or nearby, and adds a --with-htslib=DIR option to the configure script
# for specifying the location. It locates either an installation prefix
# (with 'include' and 'lib' subdirectories) or an HTSlib source tree, as
# HTSlib is fast-moving and users may wish to use an in-development tree.
#
# Different checks occur depending on the --with-htslib argument given:
#
# With --with-htslib=DIR, checks whether DIR is a source tree or contains
# a working installation.
# By default, searches for a source tree (with a name matching htslib*)
# within or alongside $srcdir. Produces AC_MSG_ERROR if there are
# several equally-likely candidates. If there are none, checks for
# a working default installation.
# With --with-htslib=system, checks for a working default installation.
#
# If a source tree is found or specified, it is added to AC_CONFIG_SUBDIRS
# (which unfortunately may cause a "you should use literals" warning when
# autoconf is run).
#
# The following output variables are set by this macro:
#
# HTSDIR Directory containing HTSlib source tree
# HTSLIB_CPPFLAGS Preprocessor flags for compiling with HTSlib
# HTSLIB_LDFLAGS Linker flags for linking with HTSlib
#
# The following shell variables may be defined:
#
# ax_cv_htslib Set to "yes" if HTSlib was found
# ax_cv_htslib_which Set to "source", "install", or "none"
#
# LICENSE
#
# Copyright (C) 2015 Genome Research Ltd
#
# Copying and distribution of this file, with or without modification, are
# permitted in any medium without royalty provided the copyright notice
# and this notice are preserved. This file is offered as-is, without any
# warranty.
#serial 1
AC_DEFUN([AX_WITH_HTSLIB],
[AC_ARG_WITH([htslib],
[AS_HELP_STRING([--with-htslib=DIR],
[use the HTSlib source tree or installation in DIR])
dnl Not indented, to avoid extra whitespace outwith AS_HELP_STRING()
AS_HELP_STRING([--with-htslib=system],
[use only a system HTSlib installation])],
[], [with_htslib=search])
case $with_htslib in
yes|search)
AC_MSG_CHECKING([location of HTSlib source tree])
case $srcdir in
.) srcp= ;;
*) srcp=$srcdir/ ;;
esac
found=
for dir in ${srcp}htslib* -- ${srcp}../htslib -- ${srcp}../htslib*
do
if test "$dir" = "--"; then
test -n "$found" && break
elif test -f "$dir/hts.c" && test -f "$dir/htslib/hts.h"; then
found="${found}1"
HTSDIR=$dir
fi
done
if test -z "$found"; then
AC_MSG_RESULT([none found])
ax_cv_htslib_which=system
elif test "$found" = 1; then
AC_MSG_RESULT([$HTSDIR])
ax_cv_htslib_which=source
else
AC_MSG_RESULT([several directories found])
AC_MSG_ERROR([use --with-htslib=DIR to select which HTSlib to use])
fi
;;
no) ax_cv_htslib_which=none ;;
system) ax_cv_htslib_which=system ;;
*)
HTSDIR=$with_htslib
if test -f "$HTSDIR/hts.c" && test -f "$HTSDIR/htslib/hts.h"; then
ax_cv_htslib_which=source
else
ax_cv_htslib_which=install
fi
;;
esac
case $ax_cv_htslib_which in
#source)
# ax_cv_htslib=yes
# HTSLIB_CPPFLAGS="-I$HTSDIR"
# HTSLIB_LDFLAGS="-L$HTSDIR"
# # We can't use a literal, because $HTSDIR is user-provided and variable
# AC_CONFIG_SUBDIRS($HTSDIR)
# ;;
system)
AC_CHECK_HEADER([htslib/sam.h],
[AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
[ax_cv_htslib=no], [;])
ax_cv_htslib_which=install
HTSDIR=
HTSLIB_CPPFLAGS=
HTSLIB_LDFLAGS=
;;
install)
ax_saved_CPPFLAGS=$CPPFLAGS
ax_saved_LDFLAGS=$LDFLAGS
HTSLIB_CPPFLAGS="-I$HTSDIR/include"
HTSLIB_LDFLAGS="-L$HTSDIR/lib"
CPPFLAGS="$CPPFLAGS $HTSLIB_CPPFLAGS"
LDFLAGS="$LDFLAGS $HTSLIB_LDFLAGS"
AC_CHECK_HEADER([htslib/sam.h],
[AC_CHECK_LIB(hts, hts_version, [ax_cv_htslib=yes], [ax_cv_htslib=no])],
[ax_cv_htslib=no], [;])
HTSDIR=
CPPFLAGS=$ax_saved_CPPFLAGS
LDFLAGS=$ax_saved_LDFLAGS
;;
none)
ax_cv_htslib=no
;;
esac
AC_SUBST([HTSDIR])
AC_SUBST([HTSLIB_CPPFLAGS])
AC_SUBST([HTSLIB_LDFLAGS])])

76
biology/samtools/files/patch-Makefile
View File

@ -1,33 +1,15 @@
--- Makefile.orig 2014-09-19 15:51:42 UTC
--- Makefile.orig 2015-12-15 21:26:20 UTC
+++ Makefile
@@ -21,12 +21,12 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.
-CC = gcc
-CPPFLAGS = $(DFLAGS) $(INCLUDES)
-CFLAGS = -g -Wall -O2
-LDFLAGS =
-LDLIBS =
-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
+CC ?= cc
+CPPFLAGS += $(DFLAGS) $(INCLUDES)
+CFLAGS += -Wall -Wno-unused-function -Wno-implicit-function-declaration
+LDFLAGS +=
+LDLIBS +=
+DFLAGS= -D_CURSES_LIB=1
LOBJS= bam_aux.o bam.o bam_import.o sam.o \
sam_header.o bam_plbuf.o
AOBJS= bam_index.o bam_plcmd.o sam_view.o \
@@ -39,19 +39,12 @@ AOBJS= bam_index.o bam_plcmd.o sam_
INCLUDES= -I. -I$(HTSDIR)
LIBCURSES= -lcurses # -lXCurses
@@ -39,18 +39,18 @@ 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
-prefix = /usr/local
+prefix = ${STAGEDIR}${PREFIX}
exec_prefix = $(prefix)
bindir = $(exec_prefix)/bin
-mandir = $(prefix)/share/man
datarootdir = $(prefix)/share
-mandir = $(datarootdir)/man
+mandir = $(prefix)/man
man1dir = $(mandir)/man1
@ -36,12 +18,15 @@
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_DATA = $(INSTALL) -m 644
-INSTALL_DIR = $(MKDIR_P) -m 755
-
-
PROGRAMS = samtools
+#MKDIR_P = mkdir -p
+#INSTALL = install -p
+#INSTALL_PROGRAM = $(INSTALL)
+#INSTALL_DATA = $(INSTALL) -m 644
+#INSTALL_DIR = $(MKDIR_P) -m 755
BUILT_MISC_PROGRAMS = \
@@ -59,7 +52,6 @@ BUILT_MISC_PROGRAMS = \
PROGRAMS = samtools
@@ -60,7 +60,6 @@ BUILT_MISC_PROGRAMS = \
misc/md5fa misc/md5sum-lite misc/wgsim
MISC_PROGRAMS = \
@ -49,28 +34,19 @@
misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
misc/interpolate_sam.pl misc/novo2sam.pl \
misc/plot-bamstats misc/psl2sam.pl \
@@ -82,9 +74,8 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
@@ -81,9 +80,9 @@ BUILT_TEST_PROGRAMS = \
all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS)
# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
-ALL_CPPFLAGS = $(DFLAGS) -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
+ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
-ALL_LIBS = -lz -ldl $(LIBS)
+ALL_LIBS = -lz $(LIBS)
# Adjust $(HTSDIR) to point to your top-level htslib directory
-HTSDIR = ../htslib
-include $(HTSDIR)/htslib.mk
-HTSLIB = $(HTSDIR)/libhts.a
+HTSDIR = $(prefix)/include
+HTSLIB = -lhts
BGZIP = $(HTSDIR)/bgzip
@@ -121,7 +112,7 @@ lib:libbam.a
libbam.a:$(LOBJS)
$(AR) -csru $@ $(LOBJS)
-samtools: $(AOBJS) libbam.a $(HTSLIB)
+samtools: $(AOBJS) libbam.a
$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
@@ -269,8 +260,10 @@ misc/md5sum-lite.o: misc/md5.c misc/md5.
# 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
install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
@ -80,6 +56,6 @@
+ $(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 $(DESTDIR)$(man1dir)
$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)

19
biology/samtools/files/patch-configure.ac Normal file
View File

@ -0,0 +1,19 @@
--- configure.ac.orig 2015-12-15 21:26:20 UTC
+++ configure.ac
@@ -23,12 +23,15 @@
# DEALINGS IN THE SOFTWARE.
dnl Process this file with autoconf to produce a configure script
-AC_INIT([Samtools], m4_esyscmd_s([make print-version]),
+AC_INIT([Samtools], [1.3],
[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([bamtk.c])
AC_CONFIG_HEADERS([config.h])
+m4_include([ax_with_htslib.m4])
+m4_include([ax_with_curses.m4])
+
dnl Copyright notice to be copied into the generated configure script
AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.

10
biology/samtools/files/patch-dict.c Normal file
View File

@ -0,0 +1,10 @@
--- dict.c.orig 2015-12-15 21:26:20 UTC
+++ dict.c
@@ -25,6 +25,7 @@ DEALINGS IN THE SOFTWARE. */
#include <stdio.h>
#include <zlib.h>
#include <getopt.h>
+#include <unistd.h>
#include "htslib/kseq.h"
#include "htslib/hts.h"

12
biology/samtools/files/patch-errmod.c
View File

@ -1,16 +1,14 @@
--- errmod.c.orig 2014-12-15 20:22:22 UTC
--- errmod.c.orig 2015-12-15 21:26:20 UTC
+++ errmod.c
@@ -24,6 +24,15 @@ FROM, OUT OF OR IN CONNECTION WITH THE S
@@ -24,6 +24,13 @@ FROM, OUT OF OR IN CONNECTION WITH THE S
DEALINGS IN THE SOFTWARE. */
#include <math.h>
+
+#include <sys/param.h>
+#ifdef __FreeBSD__
+# if __FreeBSD_version < 1000034
+# define logl(x) log(x)
+# define expl(x) exp(x)
+# endif
+#if defined(__FreeBSD__) && (__FreeBSD_version < 1000034)
+# define logl(x) log(x)
+# define expl(x) exp(x)
+#endif
+
#include "errmod.h"

29
biology/samtools/files/patch-test_test.pl Normal file
View File

@ -0,0 +1,29 @@
--- test/test.pl.orig 2015-12-22 22:43:15 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
my $command = $args{cmd};
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $args{redirection}");
- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
+ if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath: $out"); return; }
my @sections = ($err =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
@@ -615,7 +615,7 @@ sub test_usage_subcommand
my $commandpath = $$opts{bin}."/".$command;
my ($ret,$out,$err) = _cmd("$commandpath $subcommand $args{redirection}");
- if ( $err =~ m/\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
+ if ( $err =~ m/\/usr\/local\/bin\/bash.*no.*such/i ) { failed($opts,msg=>$test,reason=>"could not run $commandpath $subcommand: $out"); return; }
if ( $err =~ m/not.*implemented/is ) { failed($opts,msg=>$test,reason=>"subcommand indicates it is not implemented",expect_fail=>1); return; }

7
biology/samtools/files/pkg-message.in
View File

@ -1,2 +1,7 @@
The miscellaneous tools included with Samtools have been installed to
%%PREFIX%%/bin/samtools_misc
Add %%PREFIX%%/bin/samtools_misc to your path to use miscellaneous tools.
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
use them.

1
biology/samtools/pkg-plist
View File

@ -20,3 +20,4 @@ bin/samtools_misc/wgsim
bin/samtools_misc/wgsim_eval.pl
bin/samtools_misc/zoom2sam.pl
man/man1/samtools.1.gz
man/man1/wgsim.1.gz