r-ggbio: new package (#6058)

1 files changed, 69 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py
new file mode 100644
index 0000000000..56a26b4a9f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggbio/package.py
@@ -0,0 +1,69 @@
+##############################################################################
+# 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 RGgbio(RPackage):
+    """The ggbio package extends and specializes the grammar of graphics for
+       biological data. The graphics are designed to answer common scientific
+       questions, in particular those often asked of high throughput genomics
+       data. All core Bioconductor data structures are supported, where
+       appropriate. The package supports detailed views of particular genomic
+       regions, as well as genome-wide overviews. Supported overviews include
+       ideograms and grand linear views. High-level plots include sequence
+       fragment length, edge-linked interval to data view, mismatch pileup,
+       and several splicing summaries."""
+
+    homepage = "http://bioconductor.org/packages/ggbio/"
+    url      = "https://git.bioconductor.org/packages/ggbio"
+    list_url = homepage
+
+    version('1.24.1', git='https://git.bioconductor.org/packages/ggbio', commit='ef04c1bca1330f37152bcc21080cbde94849a094')
+
+    depends_on('r-gridextra', type=('build', 'run'))
+    depends_on('r-scales', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-gtable', type=('build', 'run'))
+    depends_on('r-hmisc', type=('build', 'run'))
+    depends_on('r-biovizbase', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-summarizedexperiment', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-genomicalignments', type=('build', 'run'))
+    depends_on('r-bsgenome', type=('build', 'run'))
+    depends_on('r-variantannotation', type=('build', 'run'))
+    depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-genomicfeatures', type=('build', 'run'))
+    depends_on('r-organismdbi', type=('build', 'run'))
+    depends_on('r-ggally', type=('build', 'run'))
+    depends_on('r-ensembldb', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-annotationfilter', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.24.1')