New package: r-champ (#23221)

1 files changed, 60 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-champ/package.py b/var/spack/repos/builtin/packages/r-champ/package.py
new file mode 100644
index 0000000000..478030a7c5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-champ/package.py
@@ -0,0 +1,60 @@
+# Copyright 2013-2021 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 RChamp(RPackage):
+    """Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and
+    EPIC:
+
+    The package includes quality control metrics, a selection of
+    normalization methods and novel methods to identify differentially
+    methylated regions and to highlight copy number alterations."""
+
+    bioc     = "ChAMP"
+
+    version('2.20.1', commit='99ea0463bce59f5b06bcc91f479dcd4065074896')
+
+    depends_on('r@3.3:', type=('build', 'run'))
+    depends_on('r-minfi', type=('build', 'run'))
+    depends_on('r-champdata@2.6.0:', type=('build', 'run'))
+    depends_on('r-dmrcate', type=('build', 'run'))
+    depends_on('r-illumina450probevariants-db', type=('build', 'run'))
+    depends_on('r-illuminahumanmethylationepicmanifest', type=('build', 'run'))
+    depends_on('r-dt', type=('build', 'run'))
+    depends_on('r-rpmm', type=('build', 'run'))
+    depends_on('r-prettydoc', type=('build', 'run'))
+    depends_on('r-hmisc', type=('build', 'run'))
+    depends_on('r-globaltest', type=('build', 'run'))
+    depends_on('r-sva', type=('build', 'run'))
+    depends_on('r-illuminaio', type=('build', 'run'))
+    depends_on('r-rmarkdown', type=('build', 'run'))
+    depends_on('r-illuminahumanmethylation450kmanifest', type=('build', 'run'))
+    depends_on('r-illuminahumanmethylationepicanno-ilm10b4-hg19', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
+    depends_on('r-dnacopy', type=('build', 'run'))
+    depends_on('r-preprocesscore', type=('build', 'run'))
+    depends_on('r-impute', type=('build', 'run'))
+    depends_on('r-marray', type=('build', 'run'))
+    depends_on('r-watermelon', type=('build', 'run'))
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-goseq', type=('build', 'run'))
+    depends_on('r-missmethyl', type=('build', 'run'))
+    depends_on('r-kpmt', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-qvalue', type=('build', 'run'))
+    depends_on('r-isva', type=('build', 'run'))
+    depends_on('r-doparallel', type=('build', 'run'))
+    depends_on('r-bumphunter', type=('build', 'run'))
+    depends_on('r-quadprog', type=('build', 'run'))
+    depends_on('r-shiny', type=('build', 'run'))
+    depends_on('r-shinythemes', type=('build', 'run'))
+    depends_on('r-plotly@4.5.6:', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-dendextend', type=('build', 'run'))
+    depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-combinat', type=('build', 'run'))