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deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
27 lines
997 B
Makefile
27 lines
997 B
Makefile
PORTNAME= deepTools
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DISTVERSION= 3.5.1
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CATEGORIES= biology python
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MASTER_SITES= CHEESESHOP
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PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= User-friendly tools for exploring deep-sequencing data
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/LICENSE.txt
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RUN_DEPENDS= ${PYNUMPY} \
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${PYTHON_PKGNAMEPREFIX}scipy>=0.17.0:science/py-scipy@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}matplotlib>=3.3.0:math/py-matplotlib@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}pysam>=0.14.0:biology/py-pysam@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}py2bit>=0.3.0:biology/py-py2bit@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}numpydoc>=0.5:textproc/py-numpydoc@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}pyBigWig>=0.3.18:biology/py-pybigwig@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}plotly>=4.9:graphics/py-plotly@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}deeptoolsintervals>=0.1.8:biology/py-deeptoolsintervals@${PY_FLAVOR}
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USES= python
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USE_PYTHON= autoplist concurrent distutils
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.include <bsd.port.mk>
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