First stab at organizing fs

workflow/qhtcp-workflow

@@ -807,8 +807,8 @@ qhtcp() {
     r_interactions \
       "$STUDY_DIR" \
       "$STUDY_INFO_FILE" \
-      "$STUDY_DIR/ZScores/" \
-      "$CODE_DIR/SGD_features.tab" \
+      "$STUDY_DIR/zscores/" \
+      "$APPS_DIR/r/SGD_features.tab" \
       5
   done
 
@@ -904,15 +904,15 @@ module gta
 gta() {
   debug "Running: ${FUNCNAME[0]}"
 
-  GTA_OUT_DIR="$QHTCP_PROJECT_DIR/GTAresults"
-  all_sgd_terms_csv="$CODE_DIR/All_SGD_GOTerms_for_QHTCPtk.csv" 
-  sgd_terms_tfile="$CODE_DIR/go_terms.tab"
-  sgd_features_file="$CODE_DIR/gene_association.sgd"
-  gene_ontology_file="$CODE_DIR/gene_ontology_edit.obo"
-  zscores_file="ZScores/ZScores_Interaction.csv"
+  GTA_OUT_DIR="$QHTCP_PROJECT_DIR/gta"
+  all_sgd_terms_csv="$APPS_DIR/r/All_SGD_GOTerms_for_QHTCPtk.csv" 
+  sgd_terms_tfile="$APPS_DIR/r/go_terms.tab"
+  sgd_features_file="$APPS_DIR/r/gene_association.sgd"
+  gene_ontology_file="$APPS_DIR/r/gene_ontology_edit.obo"
+  zscores_file="zscores/zscores_interaction.csv"
 
   # Sets STUDIES_NUM and NUM_STUDIES
-  get_studies
+  get_studies "$STUDY_INFO_FILE"
 
   [[ -d $GTA_OUT_DIR ]] || mkdir "$GTA_OUT_DIR"
 
@@ -958,10 +958,6 @@ gta() {
   # All studies
   # If you have an unknown # of studies it must be passed last and any preceding arguments
   # are required
-  # 
-  #
-  #
-  #
   r_gta_heatmaps \
     "$STUDY_INFO_FILE" \
     "$gene_ontology_file" \
@@ -971,7 +967,6 @@ gta() {
     "$QHTCP_PROJECT_DIR" \
     "$QHTCP_PROJECT_DIR/TermSpecificHeatmaps" \
     "${STUDIES_NUMS[@]}"
-
 }
 
 
@@ -1014,7 +1009,7 @@ r_gta() {
 
 	EOF
 
-  script="$CODE_DIR/GTAtemplate.R"
+  script="$APPS_DIR/r/GTAtemplate.R"
 
   [[ -d $5 ]] || mkdir -p "$5"
 
@@ -1051,7 +1046,7 @@ r_gta_pairwiselk() {
 
 	EOF
 
-  script="$CODE_DIR/PairwiseLK.R"
+  script="$APPS_DIR/r/PairwiseLK.R"
 
   [[ -d $4 ]] || mkdir -p "$4"