r-glimma: new package (#8940)

* r-glimma: new package

* r-glimma: git not url

* r-glimma: adding runtime deps

* r-glimma: dep types

1 files changed, 43 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py
new file mode 100644
index 0000000000..768d94bbe1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-glimma/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/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 RGlimma(RPackage):
+    """This package generates interactive visualisations for analysis of
+       RNA-sequencing data using output from limma, edgeR or DESeq2 packages
+       in an HTML page. The interactions are built on top of the popular
+       static representations of analysis results in order to provide
+       additional information."""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/Glimma.html"
+    git      = "https://git.bioconductor.org/packages/Glimma.git"
+
+    version('1.8.2', commit='f4aa1f05c2890d04b01ad4c0ab27f2f729f2c969')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.8.2:', type=('build', 'run'))
+    depends_on('r-edger', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))