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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=oH6hp+xP; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 7.61 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=oH6hp+xP; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: AB7B73B439 X-Spam-Score: 7.61 X-Migadu-Scanner: scn0.migadu.com X-TUID: cEcR1uKg5Kw9 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