r-yarn: created new package (#5925)

1 files changed, 53 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py
new file mode 100644
index 0000000000..5bb0a2bf36
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-yarn/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# 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 RYarn(RPackage):
+    """Expedite large RNA-Seq analyses using a combination of previously
+       developed tools. YARN is meant to make it easier for the user in
+       performing basic mis-annotation quality control, filtering, and
+       condition-aware normalization. YARN leverages many Bioconductor tools
+       and statistical techniques to account for the large heterogeneity and
+       sparsity found in very large RNA-seq experiments."""
+
+    homepage = "http://www.example.co://www.bioconductor.org/packages/yarn/"
+    url      = "https://git.bioconductor.org/packages/yarn"
+    list_url = homepage
+
+    version('1.2.0', git='https://git.bioconductor.org/packages/yarn', commit='28af616ef8c27dcadf6568e276dea8465486a697')
+
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-biomart', type=('build', 'run'))
+    depends_on('r-downloader', type=('build', 'run'))
+    depends_on('r-edger', type=('build', 'run'))
+    depends_on('r-gplots', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-preprocesscore', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-quantro', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.2.0')