py-mg-rast-tools: Create new package and its dependencies. (#7816)
* 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
Adam J. Stewart
parent
3274f16780
commit
f939895b1b
8 changed files with 316 additions and 0 deletions
37
var/spack/repos/builtin/packages/perl-libwww-perl/package.py
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37
var/spack/repos/builtin/packages/perl-libwww-perl/package.py
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##############################################################################
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# Copyright (c) 2013-2018, 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/spack/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 PerlLibwwwPerl(PerlPackage):
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"""The libwww-perl collection is a set of Perl modules which provides
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a simple and consistent application programming interface to the
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World-Wide Web. The main focus of the library is to provide classes and
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functions that allow you to write WWW clients."""
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homepage = "https://github.com/libwww-perl/libwww-perl"
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url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz"
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version('6.33', '2e15c1c789ac9036c99d094e47e3da23')
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50
var/spack/repos/builtin/packages/py-mg-rast-tools/package.py
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50
var/spack/repos/builtin/packages/py-mg-rast-tools/package.py
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@ -0,0 +1,50 @@
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##############################################################################
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# Copyright (c) 2013-2018, 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/spack/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 PyMgRastTools(PythonPackage):
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"""Repository of scripts and libraries for using the MG-RAST API and
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MG-RAST data."""
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homepage = "https://github.com/MG-RAST/MG-RAST-Tools"
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version('2018.04.17', git='https://github.com/MG-RAST/MG-RAST-Tools.git', commit='a40c6e6539ad0bc1c08e1b03dfc0a9759755a326')
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depends_on('perl', type=('build', 'run'))
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depends_on('py-setuptools@28.0:', type='build')
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depends_on('py-prettytable@0.7:', type=('build', 'run'))
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depends_on('py-poster@0.8.1:', type=('build', 'run'))
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depends_on('py-requests', type=('build', 'run'))
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depends_on('py-requests-toolbelt@0.8:', type=('build', 'run'))
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depends_on('py-scipy', type=('build', 'run'))
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depends_on('py-numpy', type=('build', 'run'))
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depends_on('r-matr', type=('build', 'run'))
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depends_on('shocklibs@0.1.30:')
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depends_on('perl-list-moreutils', type=('build', 'run'))
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depends_on('perl-exporter-tiny', type=('build', 'run'))
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depends_on('perl-libwww-perl', type=('build', 'run'))
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depends_on('perl-http-message', type=('build', 'run'))
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depends_on('perl-json', type=('build', 'run'))
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36
var/spack/repos/builtin/packages/py-poster/package.py
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36
var/spack/repos/builtin/packages/py-poster/package.py
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@ -0,0 +1,36 @@
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##############################################################################
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# Copyright (c) 2013-2018, 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/spack/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 PyPoster(PythonPackage):
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"""Streaming HTTP uploads and multipart/form-data encoding."""
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homepage = "https://pypi.org/project/poster/"
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url = "https://atlee.ca/software/poster/dist/0.8.1/poster-0.8.1.tar.gz"
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version('0.8.1', '2db12704538781fbaa7e63f1505d6fc8')
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depends_on('py-setuptools', type='build')
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@ -0,0 +1,38 @@
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##############################################################################
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# Copyright (c) 2013-2018, 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/spack/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 PyRequestsToolbelt(PythonPackage):
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"""A toolbelt of useful classes and functions to be used with
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python-requests"""
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homepage = "https://toolbelt.readthedocs.org/"
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url = "https://github.com/requests/toolbelt/archive/0.8.0.tar.gz"
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version('0.8.0', 'de9bf7fbcc6ae341a5c4fd9f8912bcac')
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depends_on('py-setuptools', type='build')
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depends_on('py-requests@2.0.1:3.0.0', type=('build', 'run'))
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38
var/spack/repos/builtin/packages/r-biom-utils/package.py
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var/spack/repos/builtin/packages/r-biom-utils/package.py
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##############################################################################
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# Copyright (c) 2013-2018, 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/spack/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 RBiomUtils(RPackage):
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"""Provides utilities to facilitate import, export and computation with
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the BIOM (Biological Observation Matrix) format (http://biom-format.org).
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"""
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homepage = "https://github.com/braithwaite/BIOM.utils/"
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url = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
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version('0.9', '980f08fd9848242007753cd27a998060')
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depends_on('r@3:', type=('build', 'run'))
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42
var/spack/repos/builtin/packages/r-matr/package.py
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42
var/spack/repos/builtin/packages/r-matr/package.py
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##############################################################################
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# Copyright (c) 2013-2018, 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/spack/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 RMatr(RPackage):
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"""Package matR (Metagenomics Analysis Tools for R) is an analysis
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client for the MG-RAST metagenome annotation engine, part of the US
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Department of Energy (DOE) Systems Biology Knowledge Base (KBase).
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Customized analysis and visualization tools securely access remote
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data and metadata within the popular open source R language and
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environment for statistical computing."""
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homepage = "https://github.com/MG-RAST/matR"
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url = "https://cran.r-project.org/src/contrib/Archive/matR/matR_0.9.tar.gz"
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version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a')
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depends_on('r-mgraster', type=('build', 'run'))
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depends_on('r-biom-utils', type=('build', 'run'))
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38
var/spack/repos/builtin/packages/r-mgraster/package.py
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38
var/spack/repos/builtin/packages/r-mgraster/package.py
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##############################################################################
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# Copyright (c) 2013-2018, 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/spack/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 RMgraster(RPackage):
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"""Convenience Functions for R Language Access to the v.1 API of the
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MG-RAST Metagenome Annotation Server, part of the US Department of Energy
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(DOE) Systems Biology Knowledge Base (KBase)."""
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homepage = "https://github.com/braithwaite/MGRASTer/"
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url = "https://cran.r-project.org/src/contrib/MGRASTer_0.9.tar.gz"
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version('0.9', '902c7ad4180b858d6b6428ea26d7652a')
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depends_on('r@3:', type=('build', 'run'))
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37
var/spack/repos/builtin/packages/shocklibs/package.py
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37
var/spack/repos/builtin/packages/shocklibs/package.py
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##############################################################################
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# Copyright (c) 2013-2018, 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 of99c6c1b375f7f3 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/spack/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 Shocklibs(Package):
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"""The lib for shock: An object store for scientific data."""
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homepage = "https://github.com/MG-RAST/Shock"
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url = "https://github.com/MG-RAST/Shock/archive/v0.9.24.tar.gz"
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version('0.9.24', '98b2e91e2726c7165f75afaf0ca51a5b')
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def install(self, spec, prefix):
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install_tree('libs', prefix.libs)
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