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gnu: deeptools: Deprecate in favor of python-deeptools.

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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:
Pierre Langlois 2020-06-20 18:42:04 +02:00 committed by Ludovic Courtès
parent 955caaab26
commit 3a79adab41
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GPG key ID: 090B11993D9AEBB5
1 changed files with 13 additions and 48 deletions
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61
gnu/packages/bioinformatics.scm
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@ -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")