Feature/methycode (#5374)
* methylcode: added package * pyfasta: added package * py-bsddb3: added package * py-bsddb3: added package * Update package.py * Update package.py * Update package.py * removed fixme comments * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py * Update package.py
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ynanyam
becker33
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var/spack/repos/builtin/packages/py-bsddb3/package.py
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var/spack/repos/builtin/packages/py-bsddb3/package.py
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##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PyBsddb3(PythonPackage):
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"""This module provides a nearly complete wrapping of the Oracle/Sleepycat
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C API for the Database Environment, Database, Cursor, Log Cursor,
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Sequence and Transaction objects, and each of these is exposed
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as a Python type in the bsddb3.db module."""
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homepage = "://pypi.python.org/pypi/bsddb3/6.2.5"
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url = "https://pypi.python.org/packages/ba/a7/131dfd4e3a5002ef30e20bee679d5e6bcb2fcc6af21bd5079dc1707a132c/bsddb3-6.2.5.tar.gz#md5=610267c189964c905a931990e1ba438c"
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version('6.2.5', '610267c189964c905a931990e1ba438c')
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depends_on('python@2.6:')
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depends_on('py-setuptools')
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var/spack/repos/builtin/packages/py-methylcode/package.py
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var/spack/repos/builtin/packages/py-methylcode/package.py
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##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PyMethylcode(PythonPackage):
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"""MethylCoder is a single program that takes of bisulfite-treated
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reads and outputs per-base methylation data. """
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homepage = "https://github.com/brentp/methylcode"
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url = "https://github.com/brentp/methylcode/archive/master.zip"
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version('1.0.0', 'd0ba07c1ab2c74adddd1b23f8e5823e7')
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depends_on('python@2.7.0:2.7.999')
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depends_on('py-six')
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depends_on('py-setuptools')
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depends_on('py-numpy')
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depends_on('py-pyparsing')
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depends_on('py-pyfasta')
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depends_on('py-bsddb3')
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depends_on('bowtie')
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var/spack/repos/builtin/packages/py-pyfasta/package.py
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var/spack/repos/builtin/packages/py-pyfasta/package.py
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##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PyPyfasta(PythonPackage):
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"""Pyfasta: fast, memory-efficient, pythonic (and command-line)
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access to fasta sequence files"""
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homepage = "https://pypi.python.org/pypi/pyfasta/"
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url = "https://pypi.python.org/packages/be/3f/794fbcdaaa2113f0a1d16a962463896c1a6bdab77bd63f33a8f16aae6cdc/pyfasta-0.5.2.tar.gz"
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version('0.5.2', 'bf61ab997dca329675c3eb2ee7cdfcf2')
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depends_on('python@2.6:')
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depends_on('py-setuptools')
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depends_on('py-numpy')
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