From b2d1eb5828a7c396815ea629c7f2b03bf2810fc6 Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sat, 3 Aug 2024 23:26:51 -0400 Subject: [PATCH] Fix perl modules --- workflow/qhtcp-workflow | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow index 48ebca2f..100c09c0 100755 --- a/workflow/qhtcp-workflow +++ b/workflow/qhtcp-workflow @@ -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