zhangyiss/spack
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

New package: r-champ (#23221)

Browse Source
This commit is contained in:
Glenn Johnson 2021-04-23 16:45:42 -05:00 committed by GitHub
parent 2b2a26022b
commit 5809ee6d26
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
1 changed files with 60 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

60
var/spack/repos/builtin/packages/r-champ/package.py Normal file
View File

@ -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'))