On Sun, Apr 24, 2016 at 10:27:40PM +1000, Ben Woodcroft wrote: > * gnu/packages/bioinformatics.scm (python-biom-format, > python2-biom-format): New variables.
LGTM! I have no opinion no the name; this seems reasonable. > --- > gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 40 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index fa67f3b..7207503 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -325,6 +325,46 @@ 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) > + (propagated-inputs > + `(("python-numpy" ,python-numpy) > + ("python-pyqi" ,python-pyqi) > + ("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) > + (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) > -- > 2.5.0 > >
