From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH 2/2] gnu: Add python-biom-format. Date: Sun, 24 Apr 2016 22:27:40 +1000 Message-ID: <1461500860-8272-3-git-send-email-donttrustben@gmail.com> References: <1461500860-8272-1-git-send-email-donttrustben@gmail.com> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55047) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1auJAa-0004rg-3x for Guix-devel@gnu.org; Sun, 24 Apr 2016 08:29:51 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1auJAW-0007Vd-UV for Guix-devel@gnu.org; Sun, 24 Apr 2016 08:29:48 -0400 Received: from mail-pf0-f193.google.com ([209.85.192.193]:33537) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1auJAW-0007VQ-Pz for Guix-devel@gnu.org; Sun, 24 Apr 2016 08:29:44 -0400 Received: by mail-pf0-f193.google.com with SMTP id e190so14771523pfe.0 for ; Sun, 24 Apr 2016 05:29:44 -0700 (PDT) Received: from localhost.localdomain ([103.25.181.216]) by smtp.googlemail.com with ESMTPSA id zs16sm11248433pab.13.2016.04.24.05.28.56 for (version=TLS1_2 cipher=ECDHE-RSA-AES128-SHA bits=128/128); Sun, 24 Apr 2016 05:28:58 -0700 (PDT) In-Reply-To: <1461500860-8272-1-git-send-email-donttrustben@gmail.com> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Guix-devel@gnu.org * gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format): New variables. --- 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