From 95da97e7fc481422d6f0ddf2ca23c627db642056 Mon Sep 17 00:00:00 2001
From: Bryan Roessler <bryanroessler@gmail.com>
Date: Sat, 3 Aug 2024 23:21:15 -0400
Subject: [PATCH] Fix perl modules

---
 workflow/qhtcp-workflow | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/workflow/qhtcp-workflow b/workflow/qhtcp-workflow
index 3b95dc1f..48ebca2f 100755
--- a/workflow/qhtcp-workflow
+++ b/workflow/qhtcp-workflow
@@ -380,6 +380,7 @@ interactive_header() {
         echo "$line" >> ~/.bashrc
       fi
     fi
+    declare -gx R_LIBS_USER="$HOME/R/$SCRIPT_NAME"
   else
     debug "R_LIBS_USER already set to $HOME/R/$SCRIPT_NAME"
   fi
@@ -584,14 +585,14 @@ install_dependencies() {
   
   # 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(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")}"
+  debug "$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
   for d in "${depends_bioc[@]}"; do
-    debug "$RSCRIPT -e \"BiocManager::install(\"$d\")\""
-    "$RSCRIPT" -e "BiocManager::install(\"$d\")"
+    debug "$RSCRIPT -e \"BiocManager::install(\"$d\", lib=\"$R_LIBS_USER\")\""
+    "$RSCRIPT" -e "BiocManager::install(\"$d\", lib=\"$R_LIBS_USER\")"
   done
 
   hash "$MATLAB" &>/dev/null || echo "You will also need MATLAB installed for GUI modules"
@@ -678,6 +679,7 @@ module easy
 # * Don't create output in the scans folder, put it in an output directory
 # * The !!Results output files need standardized naming
 # * The input MasterPlate and DrugMedia sheets need to be converted to something standard like csv/tsv
+# * This would allow them to be created programmatically as well
 #
 # NOTES
 #
@@ -2066,6 +2068,7 @@ main() {
     declare -gx STUDY_TEMPLATE_DIR="$TEMPLATES_DIR/exp"
     declare -gx STUDY_INFO_FILE="$QHTCP_PROJECT_DIR/StudyInfo.csv"
     declare -gx EASY_OUT_DIR="$QHTCP_PROJECT_DIR/easy"
+    declare -gx R_LIBS_USER=${R_LIBS_USER:-"$HOME/R/$SCRIPT_NAME"}
     if ((DEBUG)); then
       declare -p SCANS_DIR OUT_DIR TEMPLATES_DIR APPS_DIR \
       PROJECTS PROJECT_NAME \