git: 5a2a6eb32954 - main - biology/peak-classifier: Classify peaks based on GFF features

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=5a2a6eb32954aa49c79269b08fd7e26ca4436f3d

commit 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-06-14 16:40:33 +0000
Commit:     Jason W. Bacon <jwb at FreeBSD.org>
CommitDate: 2021-06-14 16:40:33 +0000

    biology/peak-classifier: Classify peaks based on GFF features
    
    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.
---
 biology/Makefile                  |  1 +
 biology/peak-classifier/Makefile  | 24 ++++++++++++++++++++++++
 biology/peak-classifier/distinfo  |  3 +++
 biology/peak-classifier/pkg-descr |  8 ++++++++
 biology/peak-classifier/pkg-plist |  9 +++++++++
 5 files changed, 45 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 4025c269aef3..4acd54fab965 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -112,6 +112,7 @@
     SUBDIR += paml
     SUBDIR += pbbam
     SUBDIR += pbseqan
+    SUBDIR += peak-classifier
     SUBDIR += pear-merger
     SUBDIR += phrap
     SUBDIR += phred
diff --git a/biology/peak-classifier/Makefile b/biology/peak-classifier/Makefile
new file mode 100644
index 000000000000..e964f1b7b49a
--- /dev/null
+++ b/biology/peak-classifier/Makefile
@@ -0,0 +1,24 @@
+PORTNAME=	peak-classifier
+DISTVERSION=	0.1.1
+CATEGORIES=	biology
+
+MAINTAINER=	jwb at FreeBSD.org
+COMMENT=	Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libxtend.so:devel/libxtend libbiolibc.so:biology/biolibc
+RUN_DEPENDS=	bedtools:biology/bedtools \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR}
+
+USES=		localbase python:3.7+ shebangfix
+USE_GITHUB=	yes
+
+GH_ACCOUNT=	auerlab
+SHEBANG_FILES=	feature-view.py
+
+pre-build:
+	cd ${WRKSRC} && make depend LOCALBASE=${LOCALBASE}
+
+.include <bsd.port.mk>
diff --git a/biology/peak-classifier/distinfo b/biology/peak-classifier/distinfo
new file mode 100644
index 000000000000..43f3d37e76fb
--- /dev/null
+++ b/biology/peak-classifier/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1623687381
+SHA256 (auerlab-peak-classifier-0.1.1_GH0.tar.gz) = 45230d50f204ecf1fa0f8bb1c96f00c25d84ae592b8def1cf053a07de60a8c7b
+SIZE (auerlab-peak-classifier-0.1.1_GH0.tar.gz) = 86012
diff --git a/biology/peak-classifier/pkg-descr b/biology/peak-classifier/pkg-descr
new file mode 100644
index 000000000000..b123dcbc554d
--- /dev/null
+++ b/biology/peak-classifier/pkg-descr
@@ -0,0 +1,8 @@
+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.
+
+WWW: https://github.com/auerlab/peak-classifier
diff --git a/biology/peak-classifier/pkg-plist b/biology/peak-classifier/pkg-plist
new file mode 100644
index 000000000000..787333471195
--- /dev/null
+++ b/biology/peak-classifier/pkg-plist
@@ -0,0 +1,9 @@
+bin/extract-genes
+bin/feature-view
+bin/filter-overlaps
+bin/peak-classifier
+libexec/extract-genes.awk
+man/man1/extract-genes.1.gz
+man/man1/feature-view.1.gz
+man/man1/filter-overlaps.1.gz
+man/man1/peak-classifier.1.gz