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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c3ba9634ba..80721b8797 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -380,6 +380,55 @@ pybedtools extends BEDTools by offering feature-level manipulations from with Python.") (license license:gpl2+))) +(define-public python-biom-format + (package + (name "python-biom-format") + (version "2.1.5") + (source + (origin + (method url-fetch) + ;; Use GitHub as source because PyPI distribution does not contain + ;; test data: https://github.com/biocore/biom-format/issues/693 + (uri (string-append "https://github.com/biocore/biom-format/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278")))) + (build-system python-build-system) + (inputs + `(("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-future" ,python-future) + ("python-click" ,python-click) + ("python-h5py" ,python-h5py))) + (home-page "http://www.biom-format.org") + (synopsis "Biological Observation Matrix (BIOM) format utilities") + (description + "The BIOM file format is designed to be a general-use format for +representing counts of observations e.g. operational taxonomic units, KEGG +orthology groups or lipid types, in one or more biological samples +e.g. microbiome samples, genomes, metagenomes.") + (license license:bsd-3) + (properties `((python2-variant . ,(delay python2-biom-format)))))) + +(define-public python2-biom-format + (let ((base (package-with-python2 (strip-python2-variant python-biom-format)))) + (package + (inherit base) + (arguments + `(#:phases + (modify-phases %standard-phases + ;; Do not require the unmaintained pyqi library. + (add-after 'unpack 'remove-pyqi + (lambda _ + (substitute* "setup.py" + (("install_requires.append\\(\"pyqi\"\\)") "pass")) + #t))) + ,@(package-arguments base))) + (native-inputs `(("python2-setuptools" ,python2-setuptools) + ,@(package-native-inputs base)))))) + (define-public bioperl-minimal (let* ((inputs `(("perl-module-build" ,perl-module-build) ("perl-data-stag" ,perl-data-stag) |