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Use a custom local R library

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Bryan Roessler
2024-08-01 23:38:46 -04:00
parent 45c47ed1d2
commit f77e8026e1
1 changed files with 5 additions and 2 deletions
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7
workflow/qhtcp-workflow
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@@ -66,7 +66,7 @@ shopt -s extglob
JAVA="${JAVA:-java}" JAVA="${JAVA:-java}"
PYTHON="${PYTHON:-python3}" PYTHON="${PYTHON:-python3}"
PERL="${PERL:-perl}" PERL="${PERL:-perl}"
RSCRIPT="${RSCRIPT:-Rscript}" RSCRIPT="${RSCRIPT:-"R_LIBS_USER=~/R/qhtcp-workflow Rscript=Rscript"}"
# @section Help # @section Help
# @description Print a helpful message # @description Print a helpful message
@@ -467,8 +467,9 @@ install_dependencies() {
# Install perl CPAN modules # Install perl CPAN modules
echo "Installing perl CPAN modules" echo "Installing perl CPAN modules"
echo "It is recommended to use the local::lib perl library if prompted"
debug "cpan -I ${depends_perl[*]}" debug "cpan -I ${depends_perl[*]}"
cpan -I "${depends_perl[@]}" cpan -I -i "${depends_perl[@]}"
# Install R packages # Install R packages
echo "Installing R packages" echo "Installing R packages"
@@ -485,6 +486,8 @@ install_dependencies() {
debug "$RSCRIPT -e install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")" debug "$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 "install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
"$RSCRIPT" -e "BiocManager::install(\"${depends_bioc[0]}\")" "$RSCRIPT" -e "BiocManager::install(\"${depends_bioc[0]}\")"
hash matlab &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
} }