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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-10-14 11:51:12 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-10-14 11:51:12 +0000 |
| commit | 799d4cc2cfd1c343f486afbde5cc735ec206de2e (patch) | |
| tree | 458c38d9907692f1e966f97af84d36e7a942d4c2 | |
| parent | 3b237ddba92c02a899db2038123dd51db549fdd2 (diff) | |
| download | ports-799d4cc2cfd1c343f486afbde5cc735ec206de2e.tar.gz ports-799d4cc2cfd1c343f486afbde5cc735ec206de2e.zip | |
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
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.
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/py-deeptools/Makefile | 26 | ||||
| -rw-r--r-- | biology/py-deeptools/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-deeptools/pkg-descr | 9 |
4 files changed, 39 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index a49bdebebeef..c4fd2890bcf3 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -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 diff --git a/biology/py-deeptools/Makefile b/biology/py-deeptools/Makefile new file mode 100644 index 000000000000..fb7dd40ad021 --- /dev/null +++ b/biology/py-deeptools/Makefile @@ -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> diff --git a/biology/py-deeptools/distinfo b/biology/py-deeptools/distinfo new file mode 100644 index 000000000000..8e524e070d7b --- /dev/null +++ b/biology/py-deeptools/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1617285775 +SHA256 (deepTools-3.5.1.tar.gz) = 62eea132513afa5f6bb51387e5866a5c3a26613aeb7e8c9600c38becf2ecb716 +SIZE (deepTools-3.5.1.tar.gz) = 199732 diff --git a/biology/py-deeptools/pkg-descr b/biology/py-deeptools/pkg-descr new file mode 100644 index 000000000000..35d810a014b3 --- /dev/null +++ b/biology/py-deeptools/pkg-descr @@ -0,0 +1,9 @@ +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 |