diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 61 |
1 files changed, 13 insertions, 48 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6c775d4baa..784fff7c09 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> +;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -53,6 +54,7 @@ #:use-module (guix build-system ruby) #:use-module (guix build-system scons) #:use-module (guix build-system trivial) + #:use-module (guix deprecation) #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages algebra) @@ -2406,12 +2408,18 @@ interval trees with associated meta-data. It is primarily used by the (name "python-deeptools") (version "3.4.3") (source (origin - (method url-fetch) - (uri (pypi-uri "deepTools" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/deepTools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb")))) + "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) (build-system python-build-system) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose))) (propagated-inputs `(("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) @@ -2436,6 +2444,8 @@ annotations of the genome.") ;; remainder of the code is licensed under the MIT license. (license (list license:bsd-3 license:expat)))) +(define-deprecated deeptools python-deeptools) + (define-public cutadapt (package (name "cutadapt") @@ -2599,51 +2609,6 @@ trees (phylogenies) and characters.") with Python.") (license license:expat))) -(define-public deeptools - (package - (name "deeptools") - (version "3.1.3") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/deepTools.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This phase fails, but it's not needed. - (delete 'reset-gzip-timestamps)))) - (inputs - `(("python-plotly" ,python-plotly) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam) - ("python-py2bit" ,python-py2bit) - ("python-pybigwig" ,python-pybigwig))) - (native-inputs - `(("python-mock" ,python-mock) ;for tests - ("python-nose" ,python-nose) ;for tests - ("python-pytz" ,python-pytz))) ;for tests - (home-page "https://github.com/deeptools/deepTools") - (synopsis "Tools for normalizing and visualizing deep-sequencing data") - (description - "DeepTools addresses the challenge of handling the large amounts of data -that are now routinely generated from DNA sequencing centers. To do so, -deepTools contains useful modules to process the mapped reads data to create -coverage files in standard bedGraph and bigWig file formats. By doing so, -deepTools allows the creation of normalized coverage files or the comparison -between two files (for example, treatment and control). Finally, using such -normalized and standardized files, multiple visualizations can be created to -identify enrichments with functional annotations of the genome.") - (license license:gpl3+))) - (define-public delly (package (name "delly") |