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py-cnvkit: add new package (#7688)

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* py-cnvkit: add new package

* updating dependencies

* correcting flake8 error

* adding py-setuptools dependency
This commit is contained in:
peetsv
2018-04-10 18:25:32 -07:00
committed by Adam J. Stewart
parent 9ba7ecb1de
commit af13236d68
1 changed files with 46 additions and 0 deletions
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var/spack/repos/builtin/packages/py-cnvkit/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class PyCnvkit(PythonPackage):
"""A command-line toolkit and Python library for detecting copy number
variants and alterations genome-wide from high-throughput sequencing."""
homepage = "http://cnvkit.readthedocs.io/en/stable/"
url = "https://github.com/etal/cnvkit/archive/v0.9.2.tar.gz"
version('0.9.2', '16612c4dcc9570f6ef9fecc42caf1745')
depends_on('py-setuptools', type='build')
depends_on('py-biopython@1.62:', type=('build', 'run'))
depends_on('py-future@0.15.2:', type=('build', 'run'))
depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
depends_on('py-numpy@1.9:', type=('build', 'run'))
depends_on('py-pandas@0.18.1:', type=('build', 'run'))
depends_on('py-pyfaidx@0.4.7:', type=('build', 'run'))
depends_on('py-pysam@0.10.0:', type=('build', 'run'))
depends_on('py-reportlab@3.0:', type=('build', 'run'))
depends_on('py-scipy@0.15.0:', type=('build', 'run'))