New package: r-codex (#14869)

This PR adds the r-codex package.

- new package: r-bsgenome-hsapiens-ucsc-hg19

2 files changed, 50 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
new file mode 100644
index 0000000000..bc536f9ccd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
@@ -0,0 +1,19 @@
+# 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 RBsgenomeHsapiensUcscHg19(RPackage):
+    """Full genome sequences for Homo sapiens (Human) as provided by UCSC
+    (hg19, Feb. 2009) and stored in Biostrings objects."""
+
+    # This is a bioconductor package but there is no available git repo.
+    homepage = "http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html"
+    url      = "http://www.bioconductor.org/packages/release/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz"
+
+    version('1.4.0', sha256='88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8')
+
+    depends_on('r-bsgenome@1.33.5:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-codex/package.py b/var/spack/repos/builtin/packages/r-codex/package.py
new file mode 100644
index 0000000000..11b161ce43
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+++ b/var/spack/repos/builtin/packages/r-codex/package.py
@@ -0,0 +1,31 @@
+# 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 RCodex(RPackage):
+    """A normalization and copy number variation calling procedure for whole
+    exome DNA sequencing data. CODEX relies on the availability of multiple
+    samples processed using the same sequencing pipeline for normalization, and
+    does not require matched controls. The normalization model in CODEX
+    includes terms that specifically remove biases due to GC content, exon
+    length and targeting and amplification efficiency, and latent systemic
+    artifacts. CODEX also includes a Poisson likelihood-based recursive
+    segmentation procedure that explicitly models the count-based exome
+    sequencing data."""
+
+    homepage = "http://www.bioconductor.org/packages/release/bioc/html/CODEX.html"
+    git      = "https://git.bioconductor.org/packages/CODEX"
+
+    version('1.18.0', commit='9a95cccc7ff3fe587636317e21e39a07dddf80bc')
+
+    depends_on('r@3.2.3:', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-bsgenome-hsapiens-ucsc-hg19', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))