r-annotationhub: created new package (#5972)

1 files changed, 51 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py
new file mode 100644
index 0000000000..3b63fceaa5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# 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 RAnnotationhub(RPackage):
+    """This package provides a client for the Bioconductor AnnotationHub web
+       resource. The AnnotationHub web resource provides a central location
+       where genomic files (e.g., VCF, bed, wig) and other resources from
+       standard locations (e.g., UCSC, Ensembl) can be discovered. The
+       resource includes metadata about each resource, e.g., a textual
+       description, tags, and date of modification. The client creates and
+       manages a local cache of files retrieved by the user, helping with
+       quick and reproducible access."""
+
+    homepage = "https://bioconductor.org/packages/AnnotationHub/"
+    url      = "https://git.bioconductor.org/packages/AnnotationHub"
+    list_url = homepage
+
+    version('2.8.3', git='https://git.bioconductor.org/packages/AnnotationHub', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
+
+    depends_on('r-rsqlite', type=('build', 'run'))
+    depends_on('r-biocinstaller', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-interactivedisplaybase', type=('build', 'run'))
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-yaml', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.8.3')