Attachment #195701 for bug #230169




# $FreeBSD$

PORTNAME=	bcftools
PORTVERSION=	1.9
PORTREVISION=	1
CATEGORIES=	biology

MAINTAINER=	cartwright@asu.edu

COMMENT=	Tools for manipulating next-generation sequencing data

LICENSE=	MIT
LICENSE_FILE=	${WRKSRC}/LICENSE

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


CONFLICTS_BUILD=openssl

USES=		autoreconf gmake perl5 \
		python:env shebangfix

USE_GITHUB=	yes
GH_ACCOUNT=	samtools

USE_LDCONFIG=	yes
USE_PERL5=	test
GNU_CONFIGURE=	yes
SUB_FILES=	pkg-message
SHEBANG_FILES=	misc/* test/test.pl

OPTIONS_DEFINE=	GPL

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

post-install:
	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \
		${STAGEDIR}${PREFIX}/bin/color-chrs
	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\
	       ${STAGEDIR}${PREFIX}/bin/guess-ploidy
	${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \
		${STAGEDIR}${PREFIX}/bin/plot-roh
	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \
		${STAGEDIR}${PREFIX}/bin/run-roh
	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \
		${STAGEDIR}${PREFIX}/bin/vcfutils
	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \
		${STAGEDIR}${PREFIX}/bin/
	${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/

.include <bsd.port.mk>

Lines 1-3 Link Here

(-)biology/bcftools/distinfo (-3 / +3 lines)
1	TIMESTAMP = 1508307708	1	TIMESTAMP = 1532903716
2	SHA256 (samtools-bcftools-1.6_GH0.tar.gz) = afb2a96d3419fbe77fab5c501dc28bc5e691145353ac5600909a75c0e625f025	2	SHA256 (samtools-bcftools-1.9_GH0.tar.gz) = 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e
3	SIZE (samtools-bcftools-1.6_GH0.tar.gz) = 2333330	3	SIZE (samtools-bcftools-1.9_GH0.tar.gz) = 2394968

Lines 1-4 Link Here

(-)biology/bcftools/files/patch-Makefile (-3 / +3 lines)
1	--- Makefile.orig 2017-09-28 11:22:48 UTC	1	--- Makefile.orig 2018-07-18 08:34:29 UTC
2	+++ Makefile	2	+++ Makefile
3	@@ -22,10 +22,10 @@	3	@@ -22,10 +22,10 @@
4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER	4	# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
Lines 68-77 Link Here
68	endif	68	endif
69		69
70	bcftools: $(OBJS) $(HTSLIB)	70	bcftools: $(OBJS) $(HTSLIB)
71	@@ -273,7 +272,7 @@ docs: doc/bcftools.1 doc/bcftools.html	71	@@ -278,7 +277,7 @@ docs: doc/bcftools.1 doc/bcftools.html
72	# 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
73	# make docs can be run to update if asciidoc is available	73	# make docs can be run to update if asciidoc is available
74	install: $(PROG) $(PLUGINS)	74	install: $(PROGRAMS) $(PLUGINS)
75	- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)	75	- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
76	+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)	76	+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(misc_bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
77	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)	77	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)

Lines 1-10 Link Here

(-)biology/bcftools/files/patch-configure.ac (-2 / +2 lines)
1	--- configure.ac.orig 2017-09-28 11:22:48 UTC	1	--- configure.ac.orig 2018-07-18 08:34:29 UTC
2	+++ configure.ac	2	+++ configure.ac
3	@@ -23,7 +23,7 @@	3	@@ -23,7 +23,7 @@
4	# DEALINGS IN THE SOFTWARE.	4	# DEALINGS IN THE SOFTWARE.
5		5
6	dnl Process this file with autoconf to produce a configure script	6	dnl Process this file with autoconf to produce a configure script
7	-AC_INIT([BCFtools], m4_esyscmd_s([make print-version]),	7	-AC_INIT([BCFtools], m4_esyscmd_s([./version.sh 2>/dev/null]),
8	+AC_INIT([BCFtools], [@PORTVERSION@],	8	+AC_INIT([BCFtools], [@PORTVERSION@],
9	[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])	9	[samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
10	AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER	10	AC_PREREQ([2.63]) dnl This version introduced 4-argument AC_CHECK_HEADER

Lines 1-10 Link Here

(-)biology/bcftools/pkg-plist (-6 / +10 lines)
1	bin/bcftools	1	bin/bcftools
2	bin/samtools_misc/color-chrs.pl	2	bin/color-chrs
3	bin/samtools_misc/guess-ploidy.py	3	bin/guess-ploidy
4	bin/samtools_misc/plot-roh.py	4	bin/plot-roh
5	bin/samtools_misc/plot-vcfstats	5	bin/plot-vcfstats
6	bin/samtools_misc/run-roh.pl	6	bin/run-roh
7	bin/samtools_misc/vcfutils.pl	7	bin/vcfutils
8	libexec/bcftools/GTisec.so	8	libexec/bcftools/GTisec.so
9	libexec/bcftools/GTsubset.so	9	libexec/bcftools/GTsubset.so
10	libexec/bcftools/ad-bias.so	10	libexec/bcftools/ad-bias.so
Lines 12-17 Link Here
12	libexec/bcftools/check-ploidy.so	12	libexec/bcftools/check-ploidy.so
13	libexec/bcftools/check-sparsity.so	13	libexec/bcftools/check-sparsity.so
14	libexec/bcftools/color-chrs.so	14	libexec/bcftools/color-chrs.so
		15	libexec/bcftools/contrast.so
15	libexec/bcftools/counts.so	16	libexec/bcftools/counts.so
16	libexec/bcftools/dosage.so	17	libexec/bcftools/dosage.so
17	libexec/bcftools/fill-AN-AC.so	18	libexec/bcftools/fill-AN-AC.so
Lines 27-32 Link Here
27	libexec/bcftools/missing2ref.so	28	libexec/bcftools/missing2ref.so
28	libexec/bcftools/prune.so	29	libexec/bcftools/prune.so
29	libexec/bcftools/setGT.so	30	libexec/bcftools/setGT.so
		31	libexec/bcftools/smpl-stats.so
		32	libexec/bcftools/split.so
30	libexec/bcftools/tag2tag.so	33	libexec/bcftools/tag2tag.so
		34	libexec/bcftools/trio-stats.so
31	libexec/bcftools/trio-switch-rate.so	35	libexec/bcftools/trio-switch-rate.so
32	man/man1/bcftools.1.gz	36	man/man1/bcftools.1.gz

Return to bug 230169

Lines 2-9 Link Here

(-)biology/bcftools/Makefile (-6 / +21 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= bcftools	4	PORTNAME= bcftools
5	PORTVERSION= 1.6	5	PORTVERSION= 1.9
6	PORTREVISION= 1
7	CATEGORIES= biology	6	CATEGORIES= biology
8		7
9	MAINTAINER= cartwright@asu.edu	8	MAINTAINER= cartwright@asu.edu
Lines 10-16 Link Here
10	COMMENT= Tools for manipulating next-generation sequencing data	9	COMMENT= Tools for manipulating next-generation sequencing data
11		10
12	LICENSE= MIT	11	LICENSE= MIT
13	# LICENSE_FILE= ${WRKSRC}/LICENSE	12	LICENSE_FILE= ${WRKSRC}/LICENSE
14		13
15	BUILD_DEPENDS= htslib>=1.6:biology/htslib	14	BUILD_DEPENDS= htslib>=1.6:biology/htslib
16	LIB_DEPENDS= libhts.so:biology/htslib	15	LIB_DEPENDS= libhts.so:biology/htslib
Lines 18-30 Link Here
18		17
19	CONFLICTS_BUILD=openssl	18	CONFLICTS_BUILD=openssl
20		19
		20	USES= autoreconf gmake perl5 \
		21	python:env shebangfix
		22
21	USE_GITHUB= yes	23	USE_GITHUB= yes
22	GH_ACCOUNT= samtools	24	GH_ACCOUNT= samtools
23		25
24	USES= autoreconf gmake perl5 python:env shebangfix	26	USE_LDCONFIG= yes
25	USE_PERL5= test	27	USE_PERL5= test
26	GNU_CONFIGURE= yes	28	GNU_CONFIGURE= yes
27	SUB_FILES= pkg-message
28	SHEBANG_FILES= misc/* test/test.pl	29	SHEBANG_FILES= misc/* test/test.pl
29		30
30	OPTIONS_DEFINE= GPL	31	OPTIONS_DEFINE= GPL
Lines 46-52 Link Here
46	TEST_TARGET= test	47	TEST_TARGET= test
47		48
48	post-patch:	49	post-patch:
49	@${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' ${WRKSRC}/configure.ac	50	@${REINPLACE_CMD} -e 's\|@PORTVERSION@\|${PORTVERSION}\|g' ${WRKSRC}/configure.ac
51		51
		52	post-install:
		53	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/color-chrs.pl \
		54	${STAGEDIR}${PREFIX}/bin/color-chrs
		55	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/guess-ploidy.py\
		56	${STAGEDIR}${PREFIX}/bin/guess-ploidy
		57	${MV} /${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-roh.py \
		58	${STAGEDIR}${PREFIX}/bin/plot-roh
		59	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/run-roh.pl \
		60	${STAGEDIR}${PREFIX}/bin/run-roh
		61	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/vcfutils.pl \
		62	${STAGEDIR}${PREFIX}/bin/vcfutils
		63	${MV} ${STAGEDIR}${PREFIX}/bin/samtools_misc/plot-vcfstats \
		64	${STAGEDIR}${PREFIX}/bin/
		65	${RMDIR} ${STAGEDIR}${PREFIX}/bin/samtools_misc/
		66
52	.include <bsd.port.mk>	67	.include <bsd.port.mk>