interactions.R refactor

workflow/.vscode/extensions.json

@@ -0,0 +1,34 @@
+{
+	// See https://go.microsoft.com/fwlink/?LinkId=827846 to learn about workspace recommendations.
+	// Extension identifier format: ${publisher}.${name}. Example: vscode.csharp
+
+	// List of extensions which should be recommended for users of this workspace.
+"recommendations": [
+  "bierner.markdown-preview-github-styles",
+  "davidanson.vscode-markdownlint",
+  "dbaeumer.vscode-eslint",
+  "eamodio.gitlens",
+  "github.remotehub",
+  "github.vscode-pull-request-github",
+  "koppt.vscode-view-in-browser",
+  "mathworks.language-matlab",
+  "ms-python.debugpy",
+  "ms-python.python",
+  "ms-python.vscode-pylance",
+  "ms-vscode-remote.remote-ssh",
+  "ms-vscode.remote-explorer",
+  "ms-vscode.remote-repositories",
+  "redhat.java",
+  "redhat.vscode-yaml",
+  "reditorsupport.r",
+  "rogalmic.bash-debug",
+  "streetsidesoftware.code-spell-checker",
+  "timonwong.shellcheck",
+  "yzhang.markdown-all-in-one"
+],
+	// List of extensions recommended by VS Code that should not be recommended for users of this workspace.
+	"unwantedRecommendations": [
+		
+	]
+}
+

workflow/.vscode/launch.json

@@ -0,0 +1,50 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "type": "R-Debugger",
+      "request": "attach",
+      "name": "Attach to R process",
+      "splitOverwrittenOutput": true
+    },
+    {
+      "type": "R-Debugger",
+      "name": "Launch R-Workspace",
+      "request": "launch",
+      "debugMode": "workspace",
+      "workingDirectory": "${workspaceFolder}"
+    },
+    {
+      "type": "R-Debugger",
+      "name": "Debug R-File",
+      "request": "launch",
+      "debugMode": "file",
+      "workingDirectory": "${fileFolder}",
+      "file": "${file}",
+    },
+    {
+      "type": "R-Debugger",
+      "name": "Debug R-Function",
+      "request": "launch",
+      "debugMode": "function",
+      "workingDirectory": "${workspaceFolder}",
+      "file": "${file}",
+      "mainFunction": "main",
+      "allowGlobalDebugging": false
+    },
+    {
+      "type": "R-Debugger",
+      "name": "Debug R-Package",
+      "request": "launch",
+      "debugMode": "workspace",
+      "workingDirectory": "${workspaceFolder}",
+      "includePackageScopes": true,
+      "loadPackages": [
+        "."
+      ]
+    }
+  ]
+}

workflow/qhtcp-workflow

@@ -209,7 +209,12 @@ parse_input() {
 # @section Modules
 # @description 
 #
-# A module contains a cohesive set of actions/experiments to run on a project
+# A module contains a cohesive set of tasks, including:
+#
+# * Filesystem operations
+# * Variable setting
+# * Executing other modules
+# * Executing wrappers
 #
 # Use a module to:
 #
@@ -217,8 +222,7 @@ parse_input() {
 # * Generate project directories
 # * Group multiple wrappers (and modules) into a larger task
 # * Dictate the ordering of multiple wrappers
-# * Competently handle pushd and popd for their wrappers if they do not reside in the SCANS/PROJECT_DIR
+# * Call wrappers with the appropriate arguments
-# * Call their wrappers with the appropriate arguments
 #
 # @description
 module() { 
@@ -580,7 +584,6 @@ interactive_header() {
       unset response arr i
     done
   fi
-  echo ""
 
   # Project selection
   if [[ ${#PROJECTS[@]} -eq 0 ]]; then
@@ -685,7 +688,7 @@ install_dependencies() {
   depends_r=(
     BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2 
     plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc
-    rmarkdown plotly htmlwidgets gplots gdata)
+    rmarkdown plotly htmlwidgets gplots gdata Hmisc)
   depends_bioc=(UCSC.utils org.Sc.sgd.db)
 
   [[ $1 == "--get-depends" ]] && return 0 # if we just want to read the depends vars
@@ -693,6 +696,7 @@ install_dependencies() {
   # Install system-wide dependencies
   echo "Installing system dependencies"
   echo "You may be prompted for your sudo password to install packages using your system package manager"
+  echo "If you do not have sudo access, you may want to use toolbox"
   case "$(uname -s)" in
     Linux*|CYGWIN*|MINGW*)
       if hash dnf &>/dev/null; then
@@ -1360,9 +1364,9 @@ qhtcp() {
   # Run R interactions script on all studies
   for study in "${STUDIES[@]}"; do
     read -r num sd _ <<< "$study"
-    r_interactions "$num" "$sd" & # run in parallel, catch with wait below
+    r_interactions "$num" "$sd" &
-  done \
+  done
-  && wait -n \
+  wait -n \
   && remc \
   && gtf \
   && gta
@@ -1790,7 +1794,7 @@ r_join_interactions() {
     "${1:-$QHTCP_RESULTS_DIR}/parameters.csv"
   )
 
-  ((DEBUG)) && declare -p
+  # ((DEBUG)) && declare -p # for when the going gets tough
 
   backup "${out_files[@]}"
 
@@ -2368,6 +2372,10 @@ main() {
     fi
   done
 
+  # If module equals install_dependencies run install_dependencies
+  declare -gx R_LIBS_USER=${R_LIBS_USER:-"$HOME/R/$SCRIPT_NAME"}
+  [[ ${MODULES[*]} == "install_dependencies" ]] && install_dependencies
+
   # Loop over projects
   for PROJECT_NAME in "${PROJECTS[@]}"; do
     declare -gx PROJECT_NAME
@@ -2383,7 +2391,6 @@ main() {
     declare -gx EASY_RESULTS_DIR="$EASY_OUT_DIR/$PROJECT_PREFIX"
     declare -gx GTA_OUT_DIR="$QHTCP_RESULTS_DIR/gta"
     declare -gx GTF_OUT_DIR="$QHTCP_RESULTS_DIR/gtf"
-    declare -gx R_LIBS_USER=${R_LIBS_USER:-"$HOME/R/$SCRIPT_NAME"}
     
     # ((DEBUG)) && declare -p # for when the going gets rough
     debug "Project: $PROJECT_NAME"