peak-classifier: Classify ChIP/ATAC-Seq peaks based on features in a GFF

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun May 2 07:47:22 2021 -0500
Changeset:	ca627c93ce0eeabc786b248b20b9b757a6421294

Modified Files:
	Makefile
Added Files:
	peak-classifier/DESCR
	peak-classifier/Makefile
	peak-classifier/PLIST
	peak-classifier/distinfo

Log Message:
peak-classifier:  Classify ChIP/ATAC-Seq peaks based on features in a GFF

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
Peaks are provided in a BED file sorted by chromosome and position. The GFF
must be sorted by chromosome and position, with gene-level features separated
by ### tags and each gene organized into subfeatures such as transcripts and
exons.  This is the default for common data sources.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ca627c93ce0eeabc786b248b20b9b757a6421294

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

diffstat:
 Makefile                 |  1 +
 peak-classifier/DESCR    |  5 +++++
 peak-classifier/Makefile | 30 ++++++++++++++++++++++++++++++
 peak-classifier/PLIST    |  6 ++++++
 peak-classifier/distinfo |  6 ++++++
 5 files changed, 48 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 1d9aef7c49..0c525e98c7 100644
--- a/Makefile
+++ b/Makefile
@@ -2973,6 +2973,7 @@ SUBDIR+=	pdfminer
 SUBDIR+=	pdftk
 SUBDIR+=	pdnsd
 SUBDIR+=	pdq
+SUBDIR+=	peak-classifier
 SUBDIR+=	pear
 SUBDIR+=	pear-Base
 SUBDIR+=	pear-Cache
diff --git a/peak-classifier/DESCR b/peak-classifier/DESCR
new file mode 100644
index 0000000000..875a28de0c
--- /dev/null
+++ b/peak-classifier/DESCR
@@ -0,0 +1,5 @@
+Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
+Peaks are provided in a BED file sorted by chromosome and position. The GFF
+must be sorted by chromosome and position, with gene-level features separated
+by ### tags and each gene organized into subfeatures such as transcripts and
+exons.  This is the default for common data sources.
diff --git a/peak-classifier/Makefile b/peak-classifier/Makefile
new file mode 100644
index 0000000000..db6ab51ea5
--- /dev/null
+++ b/peak-classifier/Makefile
@@ -0,0 +1,30 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Sun May  2 07:10:29 CDT 2021               #
+###########################################################
+
+DISTNAME=	peak-classifier-0.0.1.18
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=auerlab/}
+GITHUB_TAG=	e24d4aaf208784ed5545ef8fb7ad85fea6f88820
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/auerlab/peak-classifier
+COMMENT=	Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
+LICENSE=	2-clause-bsd
+
+DEPENDS+=	${PYPKGPREFIX}-matplotlib>=3.0:../../graphics/py-matplotlib
+DEPENDS+=	bedtools>=0:../../biology/bedtools
+DEPENDS+=	coreutils>=0:../../sysutils/coreutils
+
+REPLACE_PYTHON=	feature-view.py
+
+pre-build:
+	cd ${WRKSRC} && make depend PREFIX=${PREFIX}
+
+.include "../../wip/biolibc/buildlink3.mk"
+.include "../../lang/python/application.mk"
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/peak-classifier/PLIST b/peak-classifier/PLIST
new file mode 100644
index 0000000000..9e316f0861
--- /dev/null
+++ b/peak-classifier/PLIST
@@ -0,0 +1,6 @@
+@comment $NetBSD$
+bin/feature-view
+bin/filter-overlaps
+bin/peak-classifier
+man/man1/filter-overlaps.1
+man/man1/peak-classifier.1
diff --git a/peak-classifier/distinfo b/peak-classifier/distinfo
new file mode 100644
index 0000000000..deeb44053d
--- /dev/null
+++ b/peak-classifier/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (peak-classifier-0.0.1.18-e24d4aaf208784ed5545ef8fb7ad85fea6f88820.tar.gz) = 3a92c99d6e0ad879c4a0326815357e75078854f8
+RMD160 (peak-classifier-0.0.1.18-e24d4aaf208784ed5545ef8fb7ad85fea6f88820.tar.gz) = d5566b67c5c06e428b456d3cfdfc786d5f03e2d8
+SHA512 (peak-classifier-0.0.1.18-e24d4aaf208784ed5545ef8fb7ad85fea6f88820.tar.gz) = 70d14bbf04ce7ca0f04270af51b116a367367d592a4c86242dd31b2b2494c6fa1ce4d74375a1952305a6d22c87addc54b1d90fc16704cb808f8c991f483a2355
+Size (peak-classifier-0.0.1.18-e24d4aaf208784ed5545ef8fb7ad85fea6f88820.tar.gz) = 78756 bytes