From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <46946@debbugs.gnu.org>
Subject: [bug#46946] [PATCH 2/2] gnu: Add python-cooltools.
Date: Sat, 15 Oct 2022 00:52:18 +0200 [thread overview]
Message-ID: <20221014225218.13626-2-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de>
X-Debbugs-Cc: rekado@elephly.net
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
---
gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1478ba0c46..6f228fb907 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12977,6 +12977,51 @@ (define-public python-cooler
such as Hi-C contact matrices.")
(license license:bsd-3)))
+(define-public python-cooltools
+ (package
+ (name "python-cooltools")
+ (version "0.5.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "cooltools" version))
+ (sha256
+ (base32
+ "08hyzd3kazr87nvv6rwp5i1g9rwj7jmrly925lqnvippz4wp7k4g"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (setenv "MPLCONFIGDIR" "/tmp")
+ (when tests?
+ (invoke "pytest" "-v")))))))
+ (native-inputs
+ (list python-cython
+ python-pytest))
+ (propagated-inputs
+ (list python-bioframe
+ python-click
+ python-cooler
+ python-joblib
+ python-matplotlib
+ python-multiprocess
+ python-numba
+ python-numpy
+ python-pandas
+ python-scikit-image
+ python-scikit-learn
+ python-scipy))
+ (home-page "https://github.com/open2c/cooltools")
+ (synopsis
+ "Analysis tools for genomic interaction data stored in .cool format")
+ (description
+ "This package provides necessary tools for the analysis of the genomic
+interaction data stored in @code{.cool} format. This collection of tools includes
+operations like compartment, insulation or peak calling.")
+ (license license:expat)))
+
(define-public python-hicmatrix
(package
(name "python-hicmatrix")
--
2.37.3
next prev parent reply other threads:[~2022-10-14 22:53 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-05 13:50 [bug#46946] (no subject) Mădălin Ionel Patrașcu
2021-03-05 14:19 ` [bug#46946] [PATCH 1/2] gnu: Add python-bioframe Mădălin Ionel Patrașcu
2021-03-05 14:19 ` [bug#46946] [PATCH 2/2] gnu: Add python-cooltools Mădălin Ionel Patrașcu
2021-04-01 15:38 ` [bug#46946] [PATCH 1/2] gnu: Add python-bioframe Ricardo Wurmus
2022-10-14 22:49 ` [bug#46946] [ext] " MadalinIonel.Patrascu
2022-10-14 22:52 ` [bug#46946] " Mădălin Ionel Patrașcu
2022-10-14 22:52 ` Mădălin Ionel Patrașcu [this message]
2022-11-04 12:53 ` bug#46946: Add python-bioframe, python-cooltools Ricardo Wurmus
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