Date: Thu, 14 Oct 2021 11:54:09 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 799d4cc2cfd1 - main - biology/py-deeptools: User-friendly tools for exploring deep-sequencing data Message-ID: <202110141154.19EBs96k000943@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=799d4cc2cfd1c343f486afbde5cc735ec206de2e commit 799d4cc2cfd1c343f486afbde5cc735ec206de2e Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-10-14 11:51:12 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-10-14 11:51:12 +0000 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. --- biology/Makefile | 1 + biology/py-deeptools/Makefile | 26 ++++++++++++++++++++++++++ biology/py-deeptools/distinfo | 3 +++ biology/py-deeptools/pkg-descr | 9 +++++++++ 4 files changed, 39 insertions(+) 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
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