Re: [PATCH 2/2] gnu: Add python-biom-format.

[Leo Famulari <leo@famulari.name>]

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
> 
>