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Restructure R library loading

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Bryan Roessler
2024-08-02 19:03:06 -04:00
parent b5aaf9ffb4
commit 1500eba574
1 changed files with 13 additions and 4 deletions
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@@ -433,7 +433,7 @@ install_dependencies() {
depends_r=(BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2
plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown
plotly htmlwidgets)
depends_bioc=(org.Sc.sgd.db)
depends_bioc=(UCSC.utils org.Sc.sgd.db)
[[ $1 == "--get-depends" ]] && return 0 # if we just want to read the depends vars
@@ -478,9 +478,18 @@ install_dependencies() {
}
depends_r_to_string
debug "$RSCRIPT -e install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
"$RSCRIPT" -e "install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
"$RSCRIPT" -e "BiocManager::install(\"${depends_bioc[0]}\")"
# Install R packages
for d in "${depends_r[@]}"; do
debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)); install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")\""
"$RSCRIPT" -e "if (!require(\"$d\", quietly = TRUE)); install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")"
done
# Install Bioc packages
for d in "${depends_bioc[@]}"; do
debug "$RSCRIPT -e \"BiocManager::install(\"$d\")\""
"$RSCRIPT" -e "BiocManager::install(\"$d\")"
done
hash "$MATLAB" &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
}