r-goseq: new package (#8939)

* r-goseq: new package

* r-goseq: git not url

* r-goseq: adding packages needed at runtime

* r-goseq: package type

* r-goseq: dep types

* r-goseq: one more

1 files changed, 43 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py
new file mode 100644
index 0000000000..b296d8a5db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-goseq/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 RGoseq(RPackage):
+    """Detects Gene Ontology and/or other user defined categories which are
+       over/under represented in RNA-seq data"""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/goseq.html"
+    git      = "https://git.bioconductor.org/packages/goseq.git"
+
+    version('1.32.0', commit='32fcbe647eea17d7d0d7a262610811502c421d36')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.32.0:', type=('build', 'run'))
+    depends_on('r-biasedurn', type=('build', 'run'))
+    depends_on('r-genelendatabase@1.9.2:', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))