r-annaffy: new package. (#5414)

* 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.

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'))