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r-annaffy: new package. (#5414)

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* r-annaffy: Create New Package.

* r-annaffy: Create new package.

* r-go-db: Create new package.

* r-kegg-db: Create new package.

* r-annaffy: Correct indentation.

* r-go-db: Correct indentation.

* r-kegg-db: Correct format.

* r-kegg-db: Correct format.

* r-go-db: Correct format.

* r-annaffy: Correct format.
This commit is contained in:
lingnanyuan 2017-09-28 13:49:31 -05:00 committed by Christoph Junghans
parent 3f44eb0179
commit 0bc3578dac
3 changed files with 116 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 RAnnaffy(RPackage):
"""Functions for handling data from Bioconductor Affymetrix
annotation data packages. Produces compact HTML and text
reports including experimental data and URL links to many
online databases. Allows searching biological metadata
using various criteria."""
homepage = "https://www.bioconductor.org/packages/annaffy/"
url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/annaffy_1.48.0.tar.gz"
version('1.48.0', 'c51219a222b377403fe4bc08a6c57e7f')
depends_on('r-biobase', type=('build', 'run'))
depends_on('r-go-db', type=('build', 'run'))
depends_on('r-kegg-db', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-go-db/package.py Normal file
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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 RGoDb(RPackage):
"""A set of annotation maps describing the entire Gene
Ontology assembled using data from GO."""
homepage = "https://www.bioconductor.org/packages/GO.db/"
url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/GO.db_3.4.1.tar.gz"
list_url = homepage
version('3.4.1', 'e16ee8921d8adc1ed3cbac2a3e35e386')
depends_on('r-annotationdbi', type=('build', 'run'))

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var/spack/repos/builtin/packages/r-kegg-db/package.py Normal file
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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 RKeggDb(RPackage):
"""A set of annotation maps for KEGG assembled using data from KEGG."""
homepage = "https://www.bioconductor.org/packages/KEGG.db/"
url = "https://www.bioconductor.org/packages/release/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz"
version('3.2.3', '023ac22f57063627c2e62d1ae5e011b0')
depends_on('r-annotationdbi', type=('build', 'run'))