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	pkgsrc-2023Q2-base:1.1;
locks; strict;
comment	@# @;


1.8
date	2025.03.06.01.19.03;	author bacon;	state Exp;
branches;
next	1.7;
commitid	ttX4UUbgIuqcEWLF;

1.7
date	2024.10.14.06.45.31;	author wiz;	state Exp;
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1.6
date	2023.12.23.16.35.38;	author bacon;	state Exp;
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1.5
date	2023.11.05.23.48.31;	author wiz;	state Exp;
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1.4
date	2023.08.14.05.23.51;	author wiz;	state Exp;
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1.3
date	2023.08.01.23.20.37;	author wiz;	state Exp;
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1.2
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1.1
date	2023.06.14.21.28.31;	author bacon;	state Exp;
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desc
@@


1.8
log
@Multiple packages: OWNER -> MAINTAINER
@
text
@# $NetBSD: Makefile,v 1.7 2024/10/14 06:45:31 wiz Exp $

# Update minor version when adding or removing dependencies
# Update revision for all other changes
DISTNAME=	chip-seq-1.2
CATEGORIES=	biology meta-pkgs
MASTER_SITES=	# empty

MAINTAINER=	bacon@@NetBSD.org
COMMENT=	Core tools needed for ChIP-Seq analysis

DEPENDS+=	sra-tools>0:../../biology/sra-tools
DEPENDS+=	fastq-trim>0:../../biology/fastq-trim
DEPENDS+=	fastqc>0:../../biology/fastqc
DEPENDS+=	biolibc-tools>0:../../biology/biolibc-tools
DEPENDS+=	gffread>0:../../biology/gffread
DEPENDS+=	bwa>0:../../biology/bwa
DEPENDS+=	bowtie2>0:../../biology/bowtie2
DEPENDS+=	samtools>0:../../biology/samtools
DEPENDS+=	igv>0:../../biology/igv
DEPENDS+=	${PYPKGPREFIX}-macs2>0:../../biology/py-macs2
DEPENDS+=	fasda>0:../../biology/fasda
DEPENDS+=	peak-classifier>0:../../biology/peak-classifier
DEPENDS+=	${PYPKGPREFIX}-multiqc-[0-9]*:../../biology/py-multiqc
DEPENDS+=	webbrowser>0:../../www/webbrowser
DEPENDS+=	curl>0:../../www/curl
DEPENDS+=	lz4>0:../../archivers/lz4
DEPENDS+=	xz>0:../../archivers/xz
DEPENDS+=	zstd>0:../../archivers/zstd

META_PACKAGE=	yes

.include "../../lang/python/application.mk"
.include "../../mk/bsd.pkg.mk"
@


1.7
log
@*: clean-up after python38 removal
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.6 2023/12/23 16:35:38 bacon Exp $
d9 1
a9 1
OWNER=		bacon@@NetBSD.org
@


1.6
log
@biology/chip-seq: Update to 1.2

Update python versions to match py-macs2
Add sra-tools and a few commonly used archivers to metapkg
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.5 2023/11/05 23:48:31 wiz Exp $
a32 3
# Inherited from py-macs2 dep
PYTHON_VERSIONS_INCOMPATIBLE=	27 38

@


1.5
log
@py-macs2: not for Python 3.12
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.4 2023/08/14 05:23:51 wiz Exp $
d3 3
a5 2
DISTNAME=	chip-seq-1.1
PKGREVISION=	1
d12 18
a29 12
DEPENDS+=	fastq-trim>=0:../../biology/fastq-trim
DEPENDS+=	fastqc>=0:../../biology/fastqc
DEPENDS+=	biolibc-tools>=0:../../biology/biolibc-tools
DEPENDS+=	gffread>=0:../../biology/gffread
DEPENDS+=	bwa>=0:../../biology/bwa
DEPENDS+=	bowtie2>=0:../../biology/bowtie2
DEPENDS+=	samtools>=0:../../biology/samtools
DEPENDS+=	igv>=0:../../biology/igv
DEPENDS+=	${PYPKGPREFIX}-macs2>=0:../../biology/py-macs2
DEPENDS+=	fasda>=0:../../biology/fasda
DEPENDS+=	peak-classifier>=0:../../biology/peak-classifier
DEPENDS+=	webbrowser>=0:../../www/webbrowser
d33 2
a34 1
PYTHON_VERSIONS_INCOMPATIBLE=	27 38 312
@


1.4
log
@*: recursive bump for Python 3.11 as new default
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.3 2023/08/01 23:20:37 wiz Exp $
d26 1
a26 1
PYTHON_VERSIONS_INCOMPATIBLE=	27 38
@


1.3
log
@*: remove more references to Python 3.7
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.2 2023/07/01 08:37:43 wiz Exp $
d4 1
@


1.2
log
@*: restrict py-numpy users to 3.9+ in preparation for update
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.1 2023/06/14 21:28:31 bacon Exp $
d25 1
a25 1
PYTHON_VERSIONS_INCOMPATIBLE=	27 37 38
@


1.1
log
@biology/chip-seq: Core tools needed for ChIP-Seq analysis

The chip-seq meta-package provides the core tools needed for performing
a typical ChIP-Seq differential accessibility analysis, including
adapter trimming, quality control, alignment, peak calling, and
identification of differentially accessible peaks.  Researchers may
want additional tools for data manipulation, gene ontology, etc.

Presently identical to biology/atac-seq, but may diverge in the future.
@
text
@d1 1
a1 1
# $NetBSD: Makefile,v 1.2 2023/01/29 00:33:04 wiz Exp $
d25 1
a25 1
PYTHON_VERSIONS_INCOMPATIBLE=	27 # py-macs2
@