From 8beb42e7490a2210070efc78e5ea5cb733278789 Mon Sep 17 00:00:00 2001
From: Glenn Johnson <glenn-johnson@uiowa.edu>
Date: Thu, 13 Feb 2020 20:00:39 -0600
Subject: [PATCH] New package: r-codex (#14869)
This PR adds the r-codex package.
- new package: r-bsgenome-hsapiens-ucsc-hg19
---
.../r-bsgenome-hsapiens-ucsc-hg19/package.py | 19 ++++++++++++
.../repos/builtin/packages/r-codex/package.py | 31 +++++++++++++++++++
2 files changed, 50 insertions(+)
create mode 100644 var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py
create mode 100644 var/spack/repos/builtin/packages/r-codex/package.py
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
--- /dev/null
+++ 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'))
--
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