From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <46946@debbugs.gnu.org>
Subject: [bug#46946] [PATCH 1/2] gnu: Add python-bioframe.
Date: Sat, 15 Oct 2022 00:52:17 +0200 [thread overview]
Message-ID: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <a2e7d423-e124-af29-6367-33a2b478008d@mdc-berlin.de>
X-Debbugs-Cc: rekado@elephly.net
* gnu/packages/bioinformatics.scm (python-bioframe): New variable.
---
gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++
1 file changed, 46 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f2de09aa32..1478ba0c46 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -946,6 +946,52 @@ (define (cythonized? c/c++-file)
;; licensed lgpl2.1+
(license (list license:expat license:lgpl2.1+))))
+(define-public python-bioframe
+ (package
+ (name "python-bioframe")
+ (version "0.3.3")
+ (source
+ (origin
+ (method git-fetch)
+ ;; pypi version does not contain tests and requirements.txt
+ (uri (git-reference
+ (url "https://github.com/open2c/bioframe")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "14lvb18d4npapyi6j2zqh9q94l658dzmka5riiizw1h0zb0kp9xb"))))
+ (build-system python-build-system)
+ (arguments
+ `(#: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-biopython
+ python-pysam
+ python-pytest
+ python-wheel))
+ (propagated-inputs
+ (list python-matplotlib
+ python-numpy
+ python-pandas
+ python-requests))
+ (home-page "https://github.com/open2c/bioframe")
+ (synopsis "Pandas utilities for tab-delimited and other genomic files")
+ (description
+ "This package is a library to enable flexible and scalable operations on
+genomic interval dataframes in @code{python}. @code{python-bioframe} enables
+access to a rich set of dataframe operations. Working in @code{python} enables
+rapid visualization (e.g. @code{matplotlib}, @code{seaborn}) and iteration of
+genomic analyses. The philosophy underlying @code{python-bioframe} is to enable
+flexible operations. Instead of creating a function for every possible use-case,
+we encourage users to compose functions to achieve their goals.")
+ (license license:expat)))
+
(define-public python-biom-format
(package
(name "python-biom-format")
base-commit: 10d429f2fce321d8285684503094694ec3979865
--
2.37.3
next prev parent reply other threads:[~2022-10-14 22:54 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 ` Mădălin Ionel Patrașcu [this message]
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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