gnu: deeptools: Deprecate in favor of python-deeptools.
And make sure python-deeptools's tests are running. * gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git. [native-inputs]: Add python-mock and python-nose. (deeptools): Mark as deprecated. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
This commit is contained in:
parent
955caaab26
commit
3a79adab41
|
@ -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 @@ (define-module (gnu packages bioinformatics)
|
|||
#: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 @@ (define-public python-deeptools
|
|||
(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 @@ (define-public python-deeptools
|
|||
;; 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 @@ (define-public python-py2bit
|
|||
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")
|
||||
|
|
Loading…
Reference in a new issue