freebsd-ports/biology/samtools/Makefile

# Created by: Reed A. Cartwright <cartwright@asu.edu>
# $FreeBSD$

PORTNAME=	samtools
PORTVERSION=	1.6
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
TEST_DEPENDS=	bash:shells/bash

USE_GITHUB=	yes

USES=		autoreconf gmake ncurses perl5 python:env shebangfix
USE_PERL5=	test
GNU_CONFIGURE=	yes
SUB_FILES=	pkg-message
SHEBANG_FILES=	misc/*.pl misc/*.py misc/plot-bamstats test/test.pl

CPPFLAGS+=	-I${LOCALBASE}/include
LDFLAGS+=	-L${LOCALBASE}/lib

TEST_TARGET=	test

.include <bsd.port.mk>
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> 2014-12-15 21:59:19 +00:00			`# Created by: Reed A. Cartwright <cartwright@asu.edu>`
			`# $FreeBSD$`

			`PORTNAME= samtools`
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 2017-10-25 10:19:50 +00:00			`PORTVERSION= 1.6`
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> 2014-12-15 21:59:19 +00:00			`CATEGORIES= biology`

			`MAINTAINER= cartwright@asu.edu`
			`COMMENT= Tools for manipulating next-generation sequencing data`

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

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 2017-10-25 10:19:50 +00:00			`BUILD_DEPENDS= htslib>=1.6:biology/htslib`
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c. With hat: portmgr Sponsored by: Absolight 2016-04-01 13:29:15 +00:00			`LIB_DEPENDS= libhts.so:biology/htslib`
			`TEST_DEPENDS= bash:shells/bash`
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> 2014-12-15 21:59:19 +00:00
			`USE_GITHUB= yes`

Add a USES=python:env, that will not add a dependency on Python. It has the same effect than setting PYTHON_NO_DEPENDS, but in a more compact way. Sponsored by: Absolight 2017-12-04 15:27:29 +00:00			`USES= autoreconf gmake ncurses perl5 python:env shebangfix`
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3 - 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) 2015-12-25 01:31:09 +00:00			`USE_PERL5= test`
			`GNU_CONFIGURE= yes`
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> 2014-12-15 21:59:19 +00:00			`SUB_FILES= pkg-message`
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 2017-10-25 10:19:50 +00:00			`SHEBANG_FILES= misc/.pl misc/.py misc/plot-bamstats test/test.pl`
Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> 2014-12-15 21:59:19 +00:00
			`CPPFLAGS+= -I${LOCALBASE}/include`
			`LDFLAGS+= -L${LOCALBASE}/lib`

biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3 - 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) 2015-12-25 01:31:09 +00:00			`TEST_TARGET= test`

Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu> 2014-12-15 21:59:19 +00:00			`.include <bsd.port.mk>`