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Fix perl modules

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This commit is contained in:
Bryan Roessler
2024-08-03 23:26:51 -04:00
parent 95da97e7fc
commit b2d1eb5828
1 changed files with 3 additions and 3 deletions
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workflow/qhtcp-workflow
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@@ -372,7 +372,7 @@ interactive_header() {
if [[ -z $R_LIBS_USER || $R_LIBS_USER != "$HOME/R/$SCRIPT_NAME" ]]; then
echo "This script uses a local R library at $HOME/R/$SCRIPT_NAME"
echo "You can install the R dependencies to this library using the install_dependencies module"
if ((YES)) || ask "Would you like to make this library the default for your user?"; then
if ((YES)) || ask "Would you like to make this R library the default for your user?"; then
line="export R_LIBS_USER=$HOME/R/$SCRIPT_NAME"
if ! grep -qF "$line" ~/.bashrc; then
echo "Adding $line to your .bashrc"
@@ -585,8 +585,8 @@ install_dependencies() {
# Install R packages
for d in "${depends_r[@]}"; do
debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, lib=\"$R_LIBS_USER\" repos=\"https://cloud.r-project.org\")}\""
"$RSCRIPT" -e "if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, lib=\"$R_LIBS_USER\" repos=\"https://cloud.r-project.org\")}"
debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, lib=\"$R_LIBS_USER\", repos=\"https://cloud.r-project.org\")}\""
"$RSCRIPT" -e "if (!require(\"$d\", quietly = TRUE)) {install.packages(\"$d\", dep=TRUE, lib=\"$R_LIBS_USER\", repos=\"https://cloud.r-project.org\")}"
done
# Install Bioc packages