head	1.7;
access;
symbols
	pkgsrc-2026Q1:1.7.0.10
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	pkgsrc-2025Q3:1.7.0.6
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	pkgsrc-2021Q1:1.2.0.2
	pkgsrc-2021Q1-base:1.2;
locks; strict;
comment	@# @;


1.7
date	2025.03.06.01.19.02;	author bacon;	state Exp;
branches;
next	1.6;
commitid	ttX4UUbgIuqcEWLF;

1.6
date	2023.11.08.16.46.44;	author bacon;	state Exp;
branches;
next	1.5;
commitid	MORyswU6I0JRkPLE;

1.5
date	2023.08.14.05.23.51;	author wiz;	state Exp;
branches;
next	1.4;
commitid	LOSB79OLVxvXjIAE;

1.4
date	2023.06.26.17.21.15;	author jperkin;	state Exp;
branches;
next	1.3;
commitid	3ayZhjAIAFJRRtuE;

1.3
date	2022.06.30.11.18.04;	author nia;	state Exp;
branches;
next	1.2;
commitid	AhctUV91Vubws3KD;

1.2
date	2021.02.08.01.49.25;	author bacon;	state Exp;
branches;
next	1.1;
commitid	LeuJXahXgOf3BQGC;

1.1
date	2021.01.22.17.07.50;	author bacon;	state Exp;
branches;
next	;
commitid	p2JteL9RJEs1fKEC;


desc
@@


1.7
log
@Multiple packages: OWNER -> MAINTAINER
@
text
@# $NetBSD: Makefile,v 1.6 2023/11/08 16:46:44 bacon Exp $

DISTNAME=	bedtools-2.31.1
CATEGORIES=	biology
MASTER_SITES=	${MASTER_SITE_GITHUB:=arq5x/}
GITHUB_PROJECT=	bedtools2
GITHUB_TAG=	v${PKGVERSION_NOREV}

MAINTAINER=	bacon@@NetBSD.org
HOMEPAGE=	https://bedtools.readthedocs.io/en/latest/
COMMENT=	Swiss army knife for genome arithmetic
LICENSE=	mit

USE_LANGUAGES=	c c++
USE_TOOLS+=	bash:test gmake
REPLACE_SH+=	scripts/vcfsort.sh
REPLACE_PYTHON=	scripts/makeBashScripts.py

SUBST_CLASSES+=		pybin
SUBST_STAGE.pybin=	pre-configure
SUBST_SED.pybin=	-e 's|python|${PYTHONBIN}|g'
SUBST_FILES.pybin=	Makefile

LDFLAGS.SunOS+=		-lsocket

do-test:
	cd ${WRKSRC}/test && bash test.sh

.include "../../devel/zlib/buildlink3.mk"
.include "../../archivers/bzip2/buildlink3.mk"
.include "../../archivers/xz/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../mk/bsd.pkg.mk"
@


1.6
log
@biology/bedtools: Update to 2.31.1

Code updates for modern compilers

Changes: https://github.com/arq5x/bedtools2/releases
@
text
@d1 1
a1 1
# $NetBSD$
d9 1
a9 1
OWNER=		bacon@@NetBSD.org
@


1.5
log
@*: recursive bump for Python 3.11 as new default
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.4 2023/06/26 17:21:15 jperkin Exp $
d3 1
a3 2
DISTNAME=	bedtools-2.30.0
PKGREVISION=	2
d9 1
a9 1
MAINTAINER=	bacon@@NetBSD.org
a18 2
LDFLAGS.SunOS+=	-lsocket

d24 2
@


1.4
log
@bedtools: SunOS needs libsocket.
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.3 2022/06/30 11:18:04 nia Exp $
d4 1
a4 1
PKGREVISION=	1
@


1.3
log
@*: Revbump packages that use Python at runtime without a PKGNAME prefix
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.2 2021/02/08 01:49:25 bacon Exp $
d20 2
@


1.2
log
@biology/bedtools: Update to 2.30.0

Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile
@
text
@d1 1
a1 1
# $NetBSD$
d4 1
@


1.1
log
@biology/bedtools: import bedtools-2.29.2

The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.
@
text
@d3 1
a3 1
DISTNAME=	bedtools-2.29.2
d15 1
a15 1
USE_TOOLS+=	gmake
d24 2
a25 4
# Avoid conflict with C++20 <version> by adding .txt suffix
post-extract:
	${MV} ${WRKSRC}/src/utils/gzstream/version \
		${WRKSRC}/src/utils/gzstream/version.txt
@