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Re: [PATCH 2/2] gnu: Add python-biom-format.
From: |
Leo Famulari |
Subject: |
Re: [PATCH 2/2] gnu: Add python-biom-format. |
Date: |
Mon, 25 Apr 2016 14:13:52 -0400 |
User-agent: |
Mutt/1.5.24 (2015-08-30) |
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
>
>