atac-seq: Core tools needed for ATAC-Seq analysis

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

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Jan 19 09:20:20 2023 -0600
Changeset:	9fcac3772eddf130845257e2d006bb7711a005d3

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

Log Message:
atac-seq: Core tools needed for ATAC-Seq analysis

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9fcac3772eddf130845257e2d006bb7711a005d3

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

diffstat:
 atac-seq/DESCR    |  5 +++++
 atac-seq/Makefile | 26 ++++++++++++++++++++++++++
 2 files changed, 31 insertions(+)

diffs:
diff --git a/atac-seq/DESCR b/atac-seq/DESCR
new file mode 100644
index 0000000000..97074ec25d
--- /dev/null
+++ b/atac-seq/DESCR
@@ -0,0 +1,5 @@
+The atac-seq meta-package provides the core tools needed for performing a
+typical ATAC-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/atac-seq/Makefile b/atac-seq/Makefile
new file mode 100644
index 0000000000..1dca82e989
--- /dev/null
+++ b/atac-seq/Makefile
@@ -0,0 +1,26 @@
+# $NetBSD$
+#
+
+DISTNAME=	atac-seq-1.0
+CATEGORIES=	biology meta-pkgs
+MASTER_SITES=	# empty
+
+OWNER=		bacon%NetBSD.org@localhost
+COMMENT=	Core tools needed for ATAC-Seq analysis
+
+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+=	webbrowser>=0:../../wip/webbrowser
+
+META_PACKAGE=	yes
+
+.include "../../mk/bsd.pkg.mk"