chip-seq: Test updated metapackage based on latest atac-seq

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Dec 23 10:30:30 2023 -0600
Changeset:	af8f0f7a492218c15ca5310ac417c82ce7b6c9a9

Added Files:
	chip-seq/DESCR
	chip-seq/Makefile

Log Message:
chip-seq: Test updated metapackage based on latest atac-seq

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=af8f0f7a492218c15ca5310ac417c82ce7b6c9a9

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 chip-seq/DESCR    |  6 ++++++
 chip-seq/Makefile | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+)

diffs:
diff --git a/chip-seq/DESCR b/chip-seq/DESCR
new file mode 100644
index 0000000000..f6b07c6abd
--- /dev/null
+++ b/chip-seq/DESCR
@@ -0,0 +1,6 @@
+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.
diff --git a/chip-seq/Makefile b/chip-seq/Makefile
new file mode 100644
index 0000000000..a01ec7057e
--- /dev/null
+++ b/chip-seq/Makefile
@@ -0,0 +1,37 @@
+# $NetBSD: Makefile,v 1.5 2023/11/05 23:48:31 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
+
+OWNER=		bacon%NetBSD.org@localhost
+COMMENT=	Core tools needed for ChIP-Seq analysis
+
+DEPENDS+=	sra-tools>0:../../wip/sra-tools
+DEPENDS+=	fastq-trim>0:../../wip/fastq-trim
+DEPENDS+=	fastqc>0:../../biology/fastqc
+DEPENDS+=	biolibc-tools>0:../../wip/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:../../wip/py-macs2
+DEPENDS+=	fasda>0:../../wip/fasda
+DEPENDS+=	peak-classifier>0:../../wip/peak-classifier
+DEPENDS+=	${PYPKGPREFIX}-multiqc-[0-9]*:../../wip/py-multiqc
+DEPENDS+=	webbrowser>0:../../wip/webbrowser
+DEPENDS+=	curl>0:../../www/curl
+DEPENDS+=	lz4>0:../../archivers/lz4
+DEPENDS+=	xz>0:../../archivers/xz
+DEPENDS+=	zstd>0:../../archivers/zstd
+
+META_PACKAGE=	yes
+
+# Inherited from py-macs2 dep
+PYTHON_VERSIONS_INCOMPATIBLE=	27 38
+
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"