From ccf70a80a12be86ed609ce7d37d3ae32f75edc39 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 27 Apr 2020 13:40:00 +0200 Subject: gnu: Add python-deeptools. * gnu/packages/bioinformatics.scm (python-deeptools): New variable. --- gnu/packages/bioinformatics.scm | 37 ++++++++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cd401d97f3..8ef2880472 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2015 Andreas Enge -;;; Copyright © 2016 Roel Janssen +;;; Copyright © 2016, 2020 Roel Janssen ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner ;;; Copyright © 2016, 2020 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal @@ -2355,6 +2355,41 @@ interval trees with associated meta-data. It is primarily used by the @code{deeptools} package.") (license license:expat))) +(define-public python-deeptools + (package + (name "python-deeptools") + (version "3.4.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "deepTools" version)) + (sha256 + (base32 + "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb")))) + (build-system python-build-system) + (propagated-inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-numpydoc" ,python-numpydoc) + ("python-py2bit" ,python-py2bit) + ("python-pybigwig" ,python-pybigwig) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy) + ("python-deeptoolsintervals" ,python-deeptoolsintervals) + ("python-plotly" ,python-plotly))) + (home-page "https://pypi.org/project/deepTools/") + (synopsis "Useful tools for exploring deep sequencing data") + (description "This package addresses the challenge of handling large amounts +of data that are now routinely generated from DNA sequencing centers. +@code{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. Finally, +using such normalized and standardized files, deepTools can create many +publication-ready visualizations to identify enrichments and for functional +annotations of the genome.") + ;; The file deeptools/cm.py is licensed under the BSD license. The + ;; remainder of the code is licensed under the MIT license. + (license (list license:bsd-3 license:expat)))) + (define-public cutadapt (package (name "cutadapt") -- cgit v1.2.3