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Feature/methycode (#5374)

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* 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
This commit is contained in:
ynanyam 2017-09-16 14:58:04 -05:00 committed by becker33
parent d25b159dc3
commit 5bb3538541
3 changed files with 123 additions and 0 deletions
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##############################################################################
# Copyright (c) 2013-2017, 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/llnl/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 PyBsddb3(PythonPackage):
"""This module provides a nearly complete wrapping of the Oracle/Sleepycat
C API for the Database Environment, Database, Cursor, Log Cursor,
Sequence and Transaction objects, and each of these is exposed
as a Python type in the bsddb3.db module."""
homepage = "://pypi.python.org/pypi/bsddb3/6.2.5"
url = "https://pypi.python.org/packages/ba/a7/131dfd4e3a5002ef30e20bee679d5e6bcb2fcc6af21bd5079dc1707a132c/bsddb3-6.2.5.tar.gz#md5=610267c189964c905a931990e1ba438c"
version('6.2.5', '610267c189964c905a931990e1ba438c')
depends_on('python@2.6:')
depends_on('py-setuptools')

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##############################################################################
# Copyright (c) 2013-2017, 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/llnl/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 PyMethylcode(PythonPackage):
"""MethylCoder is a single program that takes of bisulfite-treated
reads and outputs per-base methylation data. """
homepage = "https://github.com/brentp/methylcode"
url = "https://github.com/brentp/methylcode/archive/master.zip"
version('1.0.0', 'd0ba07c1ab2c74adddd1b23f8e5823e7')
depends_on('python@2.7.0:2.7.999')
depends_on('py-six')
depends_on('py-setuptools')
depends_on('py-numpy')
depends_on('py-pyparsing')
depends_on('py-pyfasta')
depends_on('py-bsddb3')
depends_on('bowtie')

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##############################################################################
# Copyright (c) 2013-2017, 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/llnl/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 PyPyfasta(PythonPackage):
"""Pyfasta: fast, memory-efficient, pythonic (and command-line)
access to fasta sequence files"""
homepage = "https://pypi.python.org/pypi/pyfasta/"
url = "https://pypi.python.org/packages/be/3f/794fbcdaaa2113f0a1d16a962463896c1a6bdab77bd63f33a8f16aae6cdc/pyfasta-0.5.2.tar.gz"
version('0.5.2', 'bf61ab997dca329675c3eb2ee7cdfcf2')
depends_on('python@2.6:')
depends_on('py-setuptools')
depends_on('py-numpy')