Cluster configuration

Configure conda miniforge environments

Download miniforge

wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

Here we need to set conda-forge as the only channel to avoid potential conflicts.

conda config --remove-key channels 2>/dev/null || true
conda config --show channels
conda config --add channels conda-forge
conda config --show channels

Install r and necessary package into python base env

mamba install -c conda-forge r-base r-tidyverse r-data.table \
    r-bh r-rcpp r-devtools r-remotes
mamba install -c conda-forge r-essentials r-ggplot2 r-data.table \
    r-tidyverse r-tictoc r-optparse r-latex2exp r-ggextra r-lattice \
    r-ggplotify r-gridgraphics r-upsetr r-ggpubr r-rcolorbrewer \
    r-devtools r-gridextra r-configr  r-envstats r-matrixcalc \
    r-mcmcpack r-truncnorm 
mamba install -c conda-forge zlib r-genio
mamba install bioconda::r-wgcna

Install R package WGCNA and BGData

install.packages("BiocManager")
BiocManager::install(c("WGCNA", "devtools"))
remotes::install_github("QuantGen/BGData")