GNU bug report logs - #46946
Add python-bioframe, python-cooltools

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <46946 <at> debbugs.gnu.org>
Subject: [bug#46946] [PATCH 2/2] gnu: Add python-cooltools.
Date: Sat, 15 Oct 2022 00:52:18 +0200

 X-Debbugs-Cc: rekado <at> 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

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