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| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2022-10-15 00:52:17 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-11-04 13:39:12 +0100 |
| commit | 14cbaac69c142b9e45c4ff111668bf187994bab8 (patch) | |
| tree | cb6fe8b5ca4faa4279917752ebb773e045736b29 | |
| parent | 12b83f697def2679a8f8bc0d6b11690bcce48e25 (diff) | |
| download | guix-14cbaac69c142b9e45c4ff111668bf187994bab8.tar.gz | |
gnu: Add python-bioframe.
X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-bioframe): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 45 |
1 files changed, 45 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8dd260f509..53daf4c2a7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |