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biology/peak-classifier: Classify peaks based on GFF features

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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.
This commit is contained in:
Jason W. Bacon 2021-06-14 11:40:33 -05:00
parent ae98b79043
commit 5a2a6eb329
5 changed files with 45 additions and 0 deletions
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1
biology/Makefile
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@ -112,6 +112,7 @@
SUBDIR += paml
SUBDIR += pbbam
SUBDIR += pbseqan
SUBDIR += peak-classifier
SUBDIR += pear-merger
SUBDIR += phrap
SUBDIR += phred

24
biology/peak-classifier/Makefile Normal file
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@ -0,0 +1,24 @@
PORTNAME= peak-classifier
DISTVERSION= 0.1.1
CATEGORIES= biology
MAINTAINER= jwb@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>

3
biology/peak-classifier/distinfo Normal file
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@ -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

8
biology/peak-classifier/pkg-descr Normal file
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@ -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

9
biology/peak-classifier/pkg-plist Normal file
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@ -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