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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-06-14 16:40:33 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-06-14 16:40:33 +0000 |
| commit | 5a2a6eb32954aa49c79269b08fd7e26ca4436f3d (patch) | |
| tree | d87041c182697fed23828290b8b6c1d0c34c38b8 /biology | |
| parent | ae98b790430fdbf2a036bb46112d6d0950d9606f (diff) | |
| download | ports-5a2a6eb32954aa49c79269b08fd7e26ca4436f3d.tar.gz ports-5a2a6eb32954aa49c79269b08fd7e26ca4436f3d.zip | |
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.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/peak-classifier/Makefile | 24 | ||||
| -rw-r--r-- | biology/peak-classifier/distinfo | 3 | ||||
| -rw-r--r-- | biology/peak-classifier/pkg-descr | 8 | ||||
| -rw-r--r-- | biology/peak-classifier/pkg-plist | 9 |
5 files changed, 45 insertions, 0 deletions
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@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 |