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authorMădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>2022-10-15 00:52:18 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-11-04 13:50:20 +0100
commit49e1a3a04b7aac1a5046f243f1320fef93effcf7 (patch)
tree3001f75e29f4fc58f31b177f92ac5dd5c0ebf666
parent14cbaac69c142b9e45c4ff111668bf187994bab8 (diff)
downloadguix-49e1a3a04b7aac1a5046f243f1320fef93effcf7.tar
guix-49e1a3a04b7aac1a5046f243f1320fef93effcf7.tar.gz
gnu: Add python-cooltools.
* gnu/packages/bioinformatics.scm (python-cooltools): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm44
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 53daf4c2a7..47f5574eeb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13035,6 +13035,50 @@ storage format, called @code{cool}, used to store genomic interaction data,
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)
+ (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")