From 0c56b598774da4ebc6ab4f5451b052927ef00d21 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Fri, 23 Apr 2021 09:28:24 -0500 Subject: [PATCH] r-dmrcate: new package (#23151) --- .../builtin/packages/r-dmrcate/package.py | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-dmrcate/package.py diff --git a/var/spack/repos/builtin/packages/r-dmrcate/package.py b/var/spack/repos/builtin/packages/r-dmrcate/package.py new file mode 100644 index 0000000000..5f04590e15 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-dmrcate/package.py @@ -0,0 +1,36 @@ +# 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 RDmrcate(RPackage): + """Methylation array and sequencing spatial analysis methods: + + De novo identification and extraction of differentially methylated regions + (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) + and Illumina Infinium Array (450K and EPIC) data. Provides functionality + for filtering probes possibly confounded by SNPs and cross-hybridisation. + Includes GRanges generation and plotting functions.""" + + bioc = "DMRcate" + + version('2.4.1', commit='bc6242a0291a9b997872f575a4417d38550c9550') + + depends_on('r@3.6.0:', type=('build', 'run')) + depends_on('r-minfi', type=('build', 'run')) + depends_on('r-summarizedexperiment', type=('build', 'run')) + depends_on('r-experimenthub', type=('build', 'run')) + depends_on('r-bsseq', type=('build', 'run')) + depends_on('r-genomeinfodb', type=('build', 'run')) + depends_on('r-limma', type=('build', 'run')) + depends_on('r-edger', type=('build', 'run')) + depends_on('r-dss', type=('build', 'run')) + depends_on('r-missmethyl', type=('build', 'run')) + depends_on('r-genomicranges', type=('build', 'run')) + depends_on('r-plyr', type=('build', 'run')) + depends_on('r-gviz', type=('build', 'run')) + depends_on('r-iranges', type=('build', 'run')) + depends_on('r-s4vectors', type=('build', 'run'))