New package: r-exomecopy (#14885)

var/spack/repos/builtin/packages/r-exomecopy/package.py

@@ -0,0 +1,24 @@
+# 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 RExomecopy(RPackage):
+    """Detection of copy number variants (CNV) from exome sequencing samples,
+    including unpaired samples. The package implements a hidden Markov model
+    which uses positional covariates, such as background read depth and
+    GC-content, to simultaneously normalize and segment the samples into
+    regions of constant copy count."""
+
+    homepage = "http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html"
+    git      = "https://git.bioconductor.org/packages/exomeCopy"
+
+    version('1.32.0', commit='c9a884427d91b6d62ddc16a939bd808e389d3ea6')
+
+    depends_on('r-iranges@2.5.27:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))