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gnu: Add python-bioframe.

X-Debbugs-Cc: rekado@elephly.net

* gnu/packages/bioinformatics.scm (python-bioframe): New variable.
master
Mădălin Ionel Patrașcu 2022-10-15 00:52:17 +02:00 committed by Ricardo Wurmus
parent 12b83f697d
commit 14cbaac69c
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@ -946,6 +946,51 @@ Python.")
;; 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 Python. Bioframe enables access to a rich set
of dataframe operations. Working in Python enables rapid visualization and
iteration of genomic analyses. The philosophy underlying 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")