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| -rw-r--r-- | var/spack/repos/builtin/packages/r-bsgenome-hsapiens-ucsc-hg19/package.py | 19 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/r-codex/package.py | 31 |
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 --- /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')) |