From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:53809) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fxYMx-0001a9-Kb for guix-patches@gnu.org; Wed, 05 Sep 2018 10:01:23 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fxYMm-0004b0-35 for guix-patches@gnu.org; Wed, 05 Sep 2018 10:01:16 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:42276) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1fxYMl-0004ZP-QM for guix-patches@gnu.org; Wed, 05 Sep 2018 10:01:07 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1fxYMl-0005CC-L0 for guix-patches@gnu.org; Wed, 05 Sep 2018 10:01:07 -0400 Subject: [bug#32642] [PATCH 14/16] gnu: Add python-cooler. Resent-Message-ID: From: Ricardo Wurmus Date: Wed, 5 Sep 2018 16:00:04 +0200 Message-ID: <20180905140006.10783-9-ricardo.wurmus@mdc-berlin.de> In-Reply-To: <20180905140006.10783-1-ricardo.wurmus@mdc-berlin.de> References: <20180905140006.10783-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 32642@debbugs.gnu.org Cc: Ricardo Wurmus * gnu/packages/bioinformatics.scm (python-cooler): New variable. --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 624bae95d..e555fb009 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13625,3 +13625,40 @@ bgzipped text file that contains a pair of genomic coordinates per line.") "This package provides procedures for efficient pythonic random access to fasta subsequences.") (license license:bsd-3))) + +(define-public python-cooler + (package + (name "python-cooler") + (version "0.7.11") + (source + (origin + (method url-fetch) + (uri (pypi-uri "cooler" version)) + (sha256 + (base32 + "08k5nxnxa6qsbk15z5z0q01n28042k87wi4905hh95rzqib15mhx")))) + (build-system python-build-system) + (propagated-inputs + `(("python-biopython" ,python-biopython) + ("python-click" ,python-click) + ("python-cytoolz" ,python-cytoolz) + ("python-dask" ,python-dask) + ("python-h5py" ,python-h5py) + ("python-multiprocess" ,python-multiprocess) + ("python-pandas" ,python-pandas) + ("python-pyfaidx" ,python-pyfaidx) + ("python-pypairix" ,python-pypairix) + ("python-pysam" ,python-pysam) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose) + ("python-numpydoc" ,python-numpydoc) + ("python-sphinx" ,python-sphinx))) + (home-page "https://github.com/mirnylab/cooler") + (synopsis "Sparse binary format for genomic interaction matrices") + (description + "Cooler is a support library for a sparse, compressed, binary persistent +storage format, called @code{cool}, used to store genomic interaction data, +such as Hi-C contact matrices.") + (license license:bsd-3))) -- 2.18.0