diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/r-annaffy/package.py | 44 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/r-go-db/package.py | 37 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/r-kegg-db/package.py | 35 |
3 files changed, 116 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py new file mode 100644 index 0000000000..7abebba8a8 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-annaffy/package.py @@ -0,0 +1,44 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py new file mode 100644 index 0000000000..62ecc68a48 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-go-db/package.py @@ -0,0 +1,37 @@ +############################################################################## +# 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')) diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py new file mode 100644 index 0000000000..17c1219ac5 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py @@ -0,0 +1,35 @@ +############################################################################## +# 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')) |