New package: r-exomedepth (#14884)

This PR adds the r-exomedepth package and r-aod as a dependency.

2 files changed, 52 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-aod/package.py b/var/spack/repos/builtin/packages/r-aod/package.py
new file mode 100644
index 0000000000..f221cf661d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-aod/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAod(RPackage):
+    """Provides a set of functions to analyse overdispersed counts or
+    proportions. Most of the methods are already available elsewhere but are
+    scattered in different packages. The proposed functions should be
+    considered as complements to more sophisticated methods such as generalized
+    estimating equations (GEE) or generalized linear mixed effect models
+    (GLMM)."""
+
+    homepage = "https://cloud.r-project.org/package=aod"
+    url      = "https://cloud.r-project.org/src/contrib/aod_1.3.1.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/aod"
+
+    version('1.3.1', sha256='052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc')
+
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-exomedepth/package.py b/var/spack/repos/builtin/packages/r-exomedepth/package.py
new file mode 100644
index 0000000000..972c92c0b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-exomedepth/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RExomedepth(RPackage):
+    """Calls copy number variants (CNVs) from targeted sequence data, typically
+    exome sequencing experiments designed to identify the genetic basis of
+    Mendelian disorders."""
+
+    homepage = "https://cloud.r-project.org/package=ExomeDepth"
+    url      = "https://cloud.r-project.org/src/contrib/ExomeDepth_1.1.15.tar.gz"
+    list_url = "https://cloud.r-project.org/src/contrib/Archive/ExomeDepth"
+
+    version('1.1.15', sha256='112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2')
+
+    depends_on('r@3.4.0:', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-genomicranges@1.23.0:', type=('build', 'run'))
+    depends_on('r-aod', type=('build', 'run'))
+    depends_on('r-vgam@0.8.4:', type=('build', 'run'))
+    depends_on('r-genomicalignments', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))