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biology/py-deeptools: User-friendly tools for exploring deep-sequencing data

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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.
This commit is contained in:
Jason W. Bacon 2021-10-14 06:51:12 -05:00
parent 3b237ddba9
commit 799d4cc2cf
4 changed files with 39 additions and 0 deletions
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1
biology/Makefile
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@ -144,6 +144,7 @@
SUBDIR += py-bx-python
SUBDIR += py-crossmap
SUBDIR += py-cutadapt
SUBDIR += py-deeptools
SUBDIR += py-deeptoolsintervals
SUBDIR += py-dnaio
SUBDIR += py-ete3

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biology/py-deeptools/Makefile Normal file
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@ -0,0 +1,26 @@
PORTNAME= deepTools
DISTVERSION= 3.5.1
CATEGORIES= biology python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= jwb@FreeBSD.org
COMMENT= User-friendly tools for exploring deep-sequencing data
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE.txt
RUN_DEPENDS= ${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}scipy>=0.17.0:science/py-scipy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}matplotlib>=3.3.0:math/py-matplotlib@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pysam>=0.14.0:biology/py-pysam@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}py2bit>=0.3.0:biology/py-py2bit@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}numpydoc>=0.5:textproc/py-numpydoc@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pyBigWig>=0.3.18:biology/py-pybigwig@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}plotly>=4.9:graphics/py-plotly@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}deeptoolsintervals>=0.1.8:biology/py-deeptoolsintervals@${PY_FLAVOR}
USES= python
USE_PYTHON= autoplist concurrent distutils
.include <bsd.port.mk>

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biology/py-deeptools/distinfo Normal file
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TIMESTAMP = 1617285775
SHA256 (deepTools-3.5.1.tar.gz) = 62eea132513afa5f6bb51387e5866a5c3a26613aeb7e8c9600c38becf2ecb716
SIZE (deepTools-3.5.1.tar.gz) = 199732

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biology/py-deeptools/pkg-descr Normal file
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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.
WWW: https://github.com/deeptools/deepTools