Attachment #187281 for bug #223094




# $FreeBSD$

PORTNAME=	bcftools
PORTVERSION=	1.6
PORTREVISION=	2
CATEGORIES=	biology

MAINTAINER=	cartwright@asu.edu

LICENSE=	MIT
# LICENSE_FILE=	${WRKSRC}/LICENSE

BUILD_DEPENDS=	htslib>=1.6:biology/htslib
LIB_DEPENDS=	libhts.so:biology/htslib
TEST_DEPENDS=	bash:shells/bash


USE_GITHUB=	yes
GH_ACCOUNT=	samtools

USES=		autoreconf gmake perl5 python shebangfix
USE_PERL5=	test
PYTHON_NO_DEPENDS=	yes
GNU_CONFIGURE=	yes
SUB_FILES=	pkg-message
SHEBANG_FILES=	misc/* test/test.pl

OPTIONS_DEFINE=	GPL
GPL_DESC=	Enable modules that rely on GPL code

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>

Lines 1-3 Link Here

(-)distinfo (-3 / +3 lines)
1	TIMESTAMP = 1463692643	1	TIMESTAMP = 1508307708
2	SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e	2	SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025
3	SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207	3	SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330




--- Makefile.orig	2017-09-28 11:22:48 UTC
+++ Makefile
@@ -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

+LDFLAGS  +=
 LIBS     =
 
 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
     OBJS += polysomy.o peakfit.o
-    GSL_LIBS = -lgsl -lcblas
+    GSL_LIBS = -lgsl -lgslcblas
 endif
 
-prefix      = /usr/local
+prefix      = ${PREFIX}
 exec_prefix = $(prefix)
 bindir      = $(exec_prefix)/bin
 libdir      = $(exec_prefix)/lib

-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
-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 = bcftools
 MISC_SCRIPTS = \
@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
 
 ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
 ALL_LDFLAGS  = $(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.
@@ -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) $(PLUGINS)
-	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
 	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
 	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
 	$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
 	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
 

Line 0 Link Here

(-)files/patch-configure.ac (+11 lines)
	1	--- configure.ac.orig 2017-09-28 11:22:48 UTC
	2	+++ configure.ac
	3	@@ -23,7 +23,7 @@
	4	# DEALINGS IN THE SOFTWARE.
	5
	6	dnl Process this file with autoconf to produce a configure script
	7	-AC_INIT([BCFtools], m4_esyscmd_s([make print-version]),
	8	+AC_INIT([BCFtools], [@PORTVERSION@],
	9	[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
	10	AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER
	11	AC_CONFIG_SRCDIR([main.c])

Line 0 Link Here

(-)files/patch-misc_run-roh.pl (+11 lines)
	1	--- misc/run-roh.pl.orig 2017-10-18 09:33:24 UTC
	2	+++ misc/run-roh.pl
	3	@@ -97,7 +97,7 @@ sub cmd
	4	else
	5	{
	6	# child
	7	- exec('/bin/bash', '-o','pipefail','-c', $cmd) or error("Failed to run the command [/bin/sh -o pipefail -c $cmd]: $!");
	8	+ exec('/bin/sh', '-c', $cmd) or error("Failed to run the command [/bin/sh -c $cmd]: $!");
	9	}
	10
	11	if ( exists($args{exit_on_error}) && !$args{exit_on_error} ) { return @out; }

Lines 1-4 Link Here

(-)files/patch-prob1.c (-1 / +1 lines)
1	--- prob1.c.orig 2015-12-15 21:42:34 UTC	1	--- prob1.c.orig 2017-09-28 11:22:48 UTC
2	+++ prob1.c	2	+++ prob1.c
3	@@ -33,6 +33,12 @@ THE SOFTWARE. */	3	@@ -33,6 +33,12 @@ THE SOFTWARE. */
4	#include <zlib.h>	4	#include <zlib.h>




--- test/test.pl.orig	2017-10-18 09:33:24 UTC
+++ test/test.pl
@@ -381,7 +381,7 @@ sub _cmd
     else
     {
         # child

     }
     return ($? >> 8, join('',@out));
 }
@@ -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");

 
     my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)|\z)/msg);
 
@@ -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");

Lines 3-7 Link Here

(-)files/pkg-message.in (-1 / +1 lines)
3		3
4	Add that directory to your path if you want to use these tools.	4	Add that directory to your path if you want to use these tools.
5		5
6	Some of these tools depend on Perl5, and it will need to be installed to	6	Some of these tools depend on Perl5/Python, and it will need to be installed to
7	use them.	7	use them.

Lines 1-19 Link Here

(-)pkg-plist (-1 / +14 lines)
1	bin/bcftools	1	bin/bcftools
2	bin/samtools_misc/color-chrs.pl	2	bin/samtools_misc/color-chrs.pl
		3	bin/samtools_misc/guess-ploidy.py
		4	bin/samtools_misc/plot-roh.py
3	bin/samtools_misc/plot-vcfstats	5	bin/samtools_misc/plot-vcfstats
		6	bin/samtools_misc/run-roh.pl
4	bin/samtools_misc/vcfutils.pl	7	bin/samtools_misc/vcfutils.pl
5	libexec/bcftools/GTisec.so	8	libexec/bcftools/GTisec.so
		9	libexec/bcftools/GTsubset.so
		10	libexec/bcftools/ad-bias.so
		11	libexec/bcftools/af-dist.so
		12	libexec/bcftools/check-ploidy.so
		13	libexec/bcftools/check-sparsity.so
6	libexec/bcftools/color-chrs.so	14	libexec/bcftools/color-chrs.so
7	libexec/bcftools/counts.so	15	libexec/bcftools/counts.so
8	libexec/bcftools/dosage.so	16	libexec/bcftools/dosage.so
9	libexec/bcftools/fill-AN-AC.so	17	libexec/bcftools/fill-AN-AC.so
		18	libexec/bcftools/fill-from-fasta.so
10	libexec/bcftools/fill-tags.so	19	libexec/bcftools/fill-tags.so
11	libexec/bcftools/fixploidy.so	20	libexec/bcftools/fixploidy.so
		21	libexec/bcftools/fixref.so
12	libexec/bcftools/frameshifts.so	22	libexec/bcftools/frameshifts.so
		23	libexec/bcftools/guess-ploidy.so
13	libexec/bcftools/impute-info.so	24	libexec/bcftools/impute-info.so
		25	libexec/bcftools/isecGT.so
14	libexec/bcftools/mendelian.so	26	libexec/bcftools/mendelian.so
15	libexec/bcftools/missing2ref.so	27	libexec/bcftools/missing2ref.so
		28	libexec/bcftools/prune.so
16	libexec/bcftools/setGT.so	29	libexec/bcftools/setGT.so
17	libexec/bcftools/tag2tag.so	30	libexec/bcftools/tag2tag.so
18	libexec/bcftools/vcf2sex.so	31	libexec/bcftools/trio-switch-rate.so
19	man/man1/bcftools.1.gz	32	man/man1/bcftools.1.gz

Return to bug 223094

Lines 2-9 Link Here

(-)Makefile (-13 / +10 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= bcftools	4	PORTNAME= bcftools
5	PORTVERSION= 1.3.1	5	PORTVERSION= 1.6
6	PORTREVISION= 2
7	CATEGORIES= biology	6	CATEGORIES= biology
8		7
9	MAINTAINER= cartwright@asu.edu	8	MAINTAINER= cartwright@asu.edu
Lines 12-18 Link Here
12	LICENSE= MIT	11	LICENSE= MIT
13	# LICENSE_FILE= ${WRKSRC}/LICENSE	12	# LICENSE_FILE= ${WRKSRC}/LICENSE
14		13
15	BUILD_DEPENDS= htslib>=1.3:biology/htslib	14	BUILD_DEPENDS= htslib>=1.6:biology/htslib
16	LIB_DEPENDS= libhts.so:biology/htslib	15	LIB_DEPENDS= libhts.so:biology/htslib
17	TEST_DEPENDS= bash:shells/bash	16	TEST_DEPENDS= bash:shells/bash
18		17
Lines 21-30 Link Here
21	USE_GITHUB= yes	20	USE_GITHUB= yes
22	GH_ACCOUNT= samtools	21	GH_ACCOUNT= samtools
23		22
24	USES= gmake perl5 shebangfix	23	USES= autoreconf gmake perl5 python shebangfix
25	USE_PERL5= test	24	USE_PERL5= test
		25	PYTHON_NO_DEPENDS= yes
		26	GNU_CONFIGURE= yes
26	SUB_FILES= pkg-message	27	SUB_FILES= pkg-message
27	SHEBANG_FILES= vcfutils.pl plot-vcfstats plugins/color-chrs.pl test/test.pl	28	SHEBANG_FILES= misc/* test/test.pl
28		29
29	OPTIONS_DEFINE= GPL	30	OPTIONS_DEFINE= GPL
30	GPL_DESC= Enable modules that rely on GPL code	31	GPL_DESC= Enable modules that rely on GPL code
Lines 37-55 Link Here
37	CPPFLAGS+= -I${LOCALBASE}/include	38	CPPFLAGS+= -I${LOCALBASE}/include
38	LDFLAGS+= -L${LOCALBASE}/lib	39	LDFLAGS+= -L${LOCALBASE}/lib
39		40
40	MAKE_ENV= INSTALL_LIB="${INSTALL_LIB}" \
41	INSTALL_DATA="${INSTALL_DATA}" \
42	INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
43	INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
44	INSTALL_DIR="${MKDIR}"
45
46	.if ${PORT_OPTIONS:MGPL}	41	.if ${PORT_OPTIONS:MGPL}
47	MAKE_ENV+= USE_GPL=1	42	MAKE_ENV+= USE_GPL=1
48	LICENSE= GPLv3	43	LICENSE= GPLv3
49	.endif	44	.endif
50		45
51	PLIST_SUB= PORTVERSION="${PORTVERSION}"
52
53	TEST_TARGET= test	46	TEST_TARGET= test
54		47
		48	post-patch:
		49	@${GREP} -q '@PORTVERSION@' ${WRKSRC}/configure.ac \|\| (echo "@PORTVERSION@ in file/patch-configure.ac is overwritten probably due to using 'make makepatch'"; exit 1)
		50	@${REINPLACE_CMD} -e 's\|@PORTVERSION@\|${PORTVERSION}\|g' ${WRKSRC}/configure.ac
		51
55	.include <bsd.port.mk>	52	.include <bsd.port.mk>

Lines 1-19 Link Here

(-)files/patch-Makefile (-45 / +46 lines)
1	--- Makefile.orig 2015-12-15 21:42:34 UTC	1	--- Makefile.orig 2017-09-28 11:22:48 UTC
2	+++ Makefile	2	+++ Makefile
3	@@ -29,16 +29,15 @@ TEST_PROG= test/test-rbuf	3	@@ -22,10 +22,10 @@
4	all: $(PROG) $(TEST_PROG)	4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
		5	# DEALINGS IN THE SOFTWARE.
5		6
6	# Adjust $(HTSDIR) to point to your top-level htslib directory
7	-HTSDIR = ../htslib
8	-include $(HTSDIR)/htslib.mk
9	-HTSLIB = $(HTSDIR)/libhts.a
10	-BGZIP = $(HTSDIR)/bgzip
11	-TABIX = $(HTSDIR)/tabix
12	+HTSDIR = $(prefix)/include
13	+HTSLIB = -lhts
14	+BGZIP = $(HTSDIR)/../bin/bgzip
15	+TABIX = $(HTSDIR)/../bin/tabix
16
17	-CC = gcc	7	-CC = gcc
18	-CPPFLAGS =	8	-CPPFLAGS =
19	-CFLAGS = -g -Wall -Wc++-compat -O2	9	-CFLAGS = -g -Wall -Wc++-compat -O2
Lines 24-40 Link Here
24	+LDFLAGS +=	14	+LDFLAGS +=
25	LIBS =	15	LIBS =
26		16
27	OBJS = main.o vcfindex.o tabix.o \	17	DYNAMIC_FLAGS = -rdynamic
28	@@ -57,26 +56,20 @@ GSL_LIBS =	18	@@ -42,26 +42,25 @@ OBJS = main.o vcfindex.o tabix.o \
29	ifdef USE_GPL	19	vcfsort.o \
30	EXTRA_CPPFLAGS += -DUSE_GPL	20	ccall.o em.o prob1.o kmin.o # the original samtools calling
31	OBJS += polysomy.o peakfit.o
32	- GSL_LIBS = -lgsl -lcblas
33	+ GSL_LIBS = -lgsl -lgslcblas
34	endif
35		21
36	-prefix = /usr/local	22	-prefix = /usr/local
37	+prefix = ${STAGEDIR}${PREFIX}	23	+prefix = ${PREFIX}
38	exec_prefix = $(prefix)	24	exec_prefix = $(prefix)
39	bindir = $(exec_prefix)/bin	25	bindir = $(exec_prefix)/bin
40	libdir = $(exec_prefix)/lib	26	libdir = $(exec_prefix)/lib
Lines 42-78 Link Here
42	-mandir = $(prefix)/share/man	28	-mandir = $(prefix)/share/man
43	+mandir = $(prefix)/man	29	+mandir = $(prefix)/man
44	man1dir = $(mandir)/man1	30	man1dir = $(mandir)/man1
45		31	# Installation location for $(PLUGINS)
46	plugindir = $(libexecdir)/bcftools	32	plugindir = $(libexecdir)/bcftools
47	pluginpath = $(plugindir)	33	pluginpath = $(plugindir)
		34	# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
		35	-misc_bindir = $(bindir)
		36	+misc_bindir = $(bindir)/samtools_misc
48		37
49	-MKDIR_P = mkdir -p	38	MKDIR_P = mkdir -p
50	-INSTALL = install -p	39	-INSTALL = install -p
51	-INSTALL_PROGRAM = $(INSTALL)
52	-INSTALL_DATA = $(INSTALL) -m 644	40	-INSTALL_DATA = $(INSTALL) -m 644
53	-INSTALL_DIR = $(MKDIR_P) -m 755	41	-INSTALL_DIR = $(MKDIR_P) -m 755
54	-	42	-INSTALL_MAN = $(INSTALL_DATA)
55	MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl	43	-INSTALL_PROGRAM = $(INSTALL)
		44	-INSTALL_SCRIPT = $(INSTALL_PROGRAM)
		45	+INSTALL_DATA = ${BSD_INSTALL_DATA}
		46	+INSTALL_DIR = $(MKDIR_P)
		47	+INSTALL_MAN = ${BSD_INSTALL_MAN}
		48	+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
		49	+INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT}
56		50
57	all:$(PROG) plugins	51	PROGRAMS = bcftools
58	@@ -181,7 +174,7 @@ test/test-rbuf: test/test-rbuf.o	52	MISC_SCRIPTS = \
59	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)	53	@@ -77,7 +76,7 @@ all: $(PROGRAMS) $(TEST_PROGRAMS) plugin
60		54
61	bcftools: $(HTSLIB) $(OBJS)	55	ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
62	- $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)	56	ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS)
63	+ $(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -pthread -lz -lm $(GSL_LIBS) $(LIBS)	57	-ALL_LIBS = -lz -ldl $(LIBS)
		58	+ALL_LIBS = -lz $(LIBS)
64		59
65	doc/bcftools.1: doc/bcftools.txt	60	# Usually config.mk and config.h are generated by running configure
66	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt	61	# or config.status, but if those aren't used create defaults here.
67	@@ -198,8 +191,9 @@ docs: doc/bcftools.1 doc/bcftools.html	62	@@ -131,7 +130,7 @@ print-version:
		63	ifdef USE_GPL
		64	main.o : EXTRA_CPPFLAGS += -DUSE_GPL
		65	OBJS += polysomy.o peakfit.o
		66	- GSL_LIBS ?= -lgsl -lcblas
		67	+ GSL_LIBS ?= -lgsl -lgslcblas
		68	endif
		69
		70	bcftools: $(OBJS) $(HTSLIB)
		71	@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html
68	# Since there is no make dependency, bcftools.1 can be out-of-date and	72	# Since there is no make dependency, bcftools.1 can be out-of-date and
69	# make docs can be run to update if asciidoc is available	73	# make docs can be run to update if asciidoc is available
70	install: $(PROG)	74	install: $(PROG) $(PLUGINS)
71	- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)	75	- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
72	- $(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)	76	+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
73	+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)	77	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
74	+ $(INSTALL_PROGRAM) $(PROG) $(DESTDIR)$(bindir)	78	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
75	+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc	79	$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
76	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
77	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
78

Lines 1-6 Link Here

(-)files/patch-test_test.pl (-4 / +4 lines)
1	--- test/test.pl.orig 2015-12-22 22:45:13 UTC	1	--- test/test.pl.orig 2017-10-18 09:33:24 UTC
2	+++ test/test.pl	2	+++ test/test.pl
3	@@ -290,7 +290,7 @@ sub _cmd	3	@@ -381,7 +381,7 @@ sub _cmd
4	else	4	else
5	{	5	{
6	# child	6	# child
Lines 9-15 Link Here
9	}	9	}
10	return ($? >> 8, join('',@out));	10	return ($? >> 8, join('',@out));
11	}	11	}
12	@@ -657,7 +657,7 @@ sub test_usage	12	@@ -782,7 +782,7 @@ sub test_usage
13	my $command = $args{cmd};	13	my $command = $args{cmd};
14	my $commandpath = $$opts{bin}."/".$command;	14	my $commandpath = $$opts{bin}."/".$command;
15	my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");	15	my ($ret,$out) = _cmd("$commandpath $args{redirection} 2>&1");
Lines 18-24 Link Here
18		18
19	my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)\|\z)/msg);	19	my @sections = ($out =~ m/(^[A-Za-z]+.*?)(?:(?=^[A-Za-z]+:)\|\z)/msg);
20		20
21	@@ -708,7 +708,7 @@ sub test_usage_subcommand	21	@@ -833,7 +833,7 @@ sub test_usage_subcommand
22	my $subcommand = $args{subcmd};	22	my $subcommand = $args{subcmd};
23	my $commandpath = $$opts{bin}."/".$command;	23	my $commandpath = $$opts{bin}."/".$command;
24	my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");	24	my ($ret,$out) = _cmd("$commandpath $subcommand $args{redirection} 2>&1");