From f77e8026e147cd152b8e41ab51a4cbb01e633435 Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Thu, 1 Aug 2024 23:38:46 -0400 Subject: [PATCH] Use a custom local R library --- workflow/qhtcp-workflow | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow index 36d72cb7..ef3bdfb6 100755 --- a/workflow/qhtcp-workflow +++ b/workflow/qhtcp-workflow @@ -66,7 +66,7 @@ shopt -s extglob JAVA="${JAVA:-java}" PYTHON="${PYTHON:-python3}" PERL="${PERL:-perl}" -RSCRIPT="${RSCRIPT:-Rscript}" +RSCRIPT="${RSCRIPT:-"R_LIBS_USER=~/R/qhtcp-workflow Rscript=Rscript"}" # @section Help # @description Print a helpful message @@ -467,8 +467,9 @@ install_dependencies() { # Install perl CPAN modules echo "Installing perl CPAN modules" + echo "It is recommended to use the local::lib perl library if prompted" debug "cpan -I ${depends_perl[*]}" - cpan -I "${depends_perl[@]}" + cpan -I -i "${depends_perl[@]}" # Install R packages echo "Installing R packages" @@ -485,6 +486,8 @@ install_dependencies() { debug "$RSCRIPT -e install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")" "$RSCRIPT" -e "install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")" "$RSCRIPT" -e "BiocManager::install(\"${depends_bioc[0]}\")" + + hash matlab &>/dev/null || echo "You will also need MATLAB installed for GUI modules" }