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py-mg-rast-tools: Create new package and its dependencies. (#7816)

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* r-matr: Create new package.

* shocklibs: Create new package.

* r-biom-utils: Create new package.

* r-mgraster: Create new package

* py-poster: Create new package.

* py-requests-toolbelt: Create new package.

* perl-libwww-perl: Create new package.

* py-mg-rast-tools: Create new package.

* mg-rast-tools: Fix version constraints for dependencies.

* Change dependency type of py-setuptools.
This commit is contained in:
lingnanyuan 2018-04-21 10:28:44 -05:00 committed by Adam J. Stewart
parent 3274f16780
commit f939895b1b
8 changed files with 316 additions and 0 deletions
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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 PerlLibwwwPerl(PerlPackage):
"""The libwww-perl collection is a set of Perl modules which provides
a simple and consistent application programming interface to the
World-Wide Web. The main focus of the library is to provide classes and
functions that allow you to write WWW clients."""
homepage = "https://github.com/libwww-perl/libwww-perl"
url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz"
version('6.33', '2e15c1c789ac9036c99d094e47e3da23')

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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 PyMgRastTools(PythonPackage):
"""Repository of scripts and libraries for using the MG-RAST API and
MG-RAST data."""
homepage = "https://github.com/MG-RAST/MG-RAST-Tools"
version('2018.04.17', git='https://github.com/MG-RAST/MG-RAST-Tools.git', commit='a40c6e6539ad0bc1c08e1b03dfc0a9759755a326')
depends_on('perl', type=('build', 'run'))
depends_on('py-setuptools@28.0:', type='build')
depends_on('py-prettytable@0.7:', type=('build', 'run'))
depends_on('py-poster@0.8.1:', type=('build', 'run'))
depends_on('py-requests', type=('build', 'run'))
depends_on('py-requests-toolbelt@0.8:', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('r-matr', type=('build', 'run'))
depends_on('shocklibs@0.1.30:')
depends_on('perl-list-moreutils', type=('build', 'run'))
depends_on('perl-exporter-tiny', type=('build', 'run'))
depends_on('perl-libwww-perl', type=('build', 'run'))
depends_on('perl-http-message', type=('build', 'run'))
depends_on('perl-json', type=('build', 'run'))

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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 PyPoster(PythonPackage):
"""Streaming HTTP uploads and multipart/form-data encoding."""
homepage = "https://pypi.org/project/poster/"
url = "https://atlee.ca/software/poster/dist/0.8.1/poster-0.8.1.tar.gz"
version('0.8.1', '2db12704538781fbaa7e63f1505d6fc8')
depends_on('py-setuptools', type='build')

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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 PyRequestsToolbelt(PythonPackage):
"""A toolbelt of useful classes and functions to be used with
python-requests"""
homepage = "https://toolbelt.readthedocs.org/"
url = "https://github.com/requests/toolbelt/archive/0.8.0.tar.gz"
version('0.8.0', 'de9bf7fbcc6ae341a5c4fd9f8912bcac')
depends_on('py-setuptools', type='build')
depends_on('py-requests@2.0.1:3.0.0', type=('build', 'run'))

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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 RBiomUtils(RPackage):
"""Provides utilities to facilitate import, export and computation with
the BIOM (Biological Observation Matrix) format (http://biom-format.org).
"""
homepage = "https://github.com/braithwaite/BIOM.utils/"
url = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
version('0.9', '980f08fd9848242007753cd27a998060')
depends_on('r@3:', type=('build', 'run'))

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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 RMatr(RPackage):
"""Package matR (Metagenomics Analysis Tools for R) is an analysis
client for the MG-RAST metagenome annotation engine, part of the US
Department of Energy (DOE) Systems Biology Knowledge Base (KBase).
Customized analysis and visualization tools securely access remote
data and metadata within the popular open source R language and
environment for statistical computing."""
homepage = "https://github.com/MG-RAST/matR"
url = "https://cran.r-project.org/src/contrib/Archive/matR/matR_0.9.tar.gz"
version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a')
depends_on('r-mgraster', type=('build', 'run'))
depends_on('r-biom-utils', type=('build', 'run'))

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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 RMgraster(RPackage):
"""Convenience Functions for R Language Access to the v.1 API of the
MG-RAST Metagenome Annotation Server, part of the US Department of Energy
(DOE) Systems Biology Knowledge Base (KBase)."""
homepage = "https://github.com/braithwaite/MGRASTer/"
url = "https://cran.r-project.org/src/contrib/MGRASTer_0.9.tar.gz"
version('0.9', '902c7ad4180b858d6b6428ea26d7652a')
depends_on('r@3:', type=('build', 'run'))

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##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of99c6c1b375f7f3 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 Shocklibs(Package):
"""The lib for shock: An object store for scientific data."""
homepage = "https://github.com/MG-RAST/Shock"
url = "https://github.com/MG-RAST/Shock/archive/v0.9.24.tar.gz"
version('0.9.24', '98b2e91e2726c7165f75afaf0ca51a5b')
def install(self, spec, prefix):
install_tree('libs', prefix.libs)