From b46bef2216620ac085bea41762904b16f2c6aec5 Mon Sep 17 00:00:00 2001
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.
---
gnu/packages/bioinformatics.scm | 61 +++++++--------------------------
1 file changed, 13 insertions(+), 48 deletions(-)
Toggle diff (105 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 95f8b16db3..580488fc49 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 K?dzio?ka <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")
--
2.26.2
