From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <46946@debbugs.gnu.org>
Cc: rekado@elephly.net,
"Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
Subject: [bug#46946] [PATCH 2/2] gnu: Add python-cooltools.
Date: Fri, 5 Mar 2021 15:19:30 +0100 [thread overview]
Message-ID: <20210305141930.28787-2-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de>
* 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 fb357b8b6c..a6ea8f831d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13652,6 +13652,51 @@ 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
+;;pypi sources requiere bioframe<0.1 while github latest version requires
+;; bioframe>=0.1.0
+ (let ((revision "1")
+ (commit "53ce4fc11d046e84ca36f3591e9e5d548de9f7b2"))
+ (package
+ (name "python-cooltools")
+ (version (git-version "0.3.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/open2c/cooltools")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0y1wf7a0by2kih2iy5xrwzdgw1i24cwigfz4352aq5npxrpjvj6q"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-bioframe" ,python-bioframe)
+ ("python-click" ,python-click)
+ ("python-cooler" ,python-cooler)
+ ("python-cytoolz" ,python-cytoolz)
+ ("python-joblib" ,python-joblib)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-multiprocess" ,python-multiprocess)
+ ("python-numba" ,python-numba)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-scikit-learn" ,python-scikit-learn)
+ ("python-scipy" ,python-scipy)
+ ("python-tables" ,python-tables)))
+ (native-inputs
+ `(("python-cython" ,python-cython)))
+ (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 .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")
--
2.30.1
next prev parent reply other threads:[~2021-03-05 14:21 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 ` Mădălin Ionel Patrașcu [this message]
2021-04-01 15:38 ` 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 ` [bug#46946] [PATCH 2/2] gnu: Add python-cooltools Mădălin Ionel Patrașcu
2022-11-04 12:53 ` bug#46946: Add python-bioframe, python-cooltools Ricardo Wurmus
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