diff --git a/msa/global.R b/msa/global.R
index 9873d8b..bc0ac57 100644
--- a/msa/global.R
+++ b/msa/global.R
@@ -31,12 +31,16 @@ library(hash)
 # than previous approaches
 
 # system.time({
-source("~/git/LSHTM_analysis/scripts/Header_TT.R")
+if(interactive()){
+  source("~/git/LSHTM_analysis/scripts/Header_TT.R")
+} else {
+  source("/srv/shiny-server/git/LSHTM_analysis/scripts/Header_TT.R")
+}
 
 load_target_globals=function(target){
   cat(paste0("Reloading Target: ", target))
   source(paste0("~/git/LSHTM_analysis/config/", target, ".R")) # load per-target config file
-
+  
   invisible(assign(paste0(target, "_merged_df3"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df3.csv")), envir = .GlobalEnv))
   invisible(assign(paste0(target, "_merged_df2"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-merged_df2.csv")), envir = .GlobalEnv))
   invisible(assign(paste0(target, "_corr_df_m3_f"), read.csv(paste0("~/git/Misc/shiny_dashboard/data/",target,"-corr_df_m3_f.csv")), envir = .GlobalEnv))
@@ -77,12 +81,12 @@ load_msa_global=function(gene){
   print(infile_msa)
   msa1 = read.csv(infile_msa, header = F)
   msa_seq = msa1$V1
-
+  
   infile_fasta = paste0("~/git/Data/", drug, "/input/", tolower(gene), "2_f2.fasta")
   print(infile_fasta)
   msa2 = read.csv(infile_fasta, header = F)
   wt_seq = msa2$V1
-
+  
   target_name=paste0(gene, '_unified_msa')
   #print(target_name)
   invisible(assign(target_name, list(msa_seq = msa_seq, wt_seq = wt_seq), envir = .GlobalEnv))
@@ -248,182 +252,182 @@ lapply(c(
 
 #### Shiny UI #####
 if(interactive()){
-ui <- dashboardPage(
-  #dashboardHeader(title = paste0(gene, "/", drug)),
-  dashboardHeader(title = "Sequence Alignment"),
-  
-  dashboardSidebar(
-    sidebarMenu( id = "sidebar",
-                 selectInput(
-                   "switch_target",
-                   label="Target",
-                   choices = c(
-                     "alr",
-                     "embb",
-                     "gid",
-                     "katg",
-                     "pnca",
-                     "rpob"
+  ui <- dashboardPage(
+    #dashboardHeader(title = paste0(gene, "/", drug)),
+    dashboardHeader(title = "Sequence Alignment"),
+    
+    dashboardSidebar(
+      sidebarMenu( id = "sidebar",
+                   selectInput(
+                     "switch_target",
+                     label="Target",
+                     choices = c(
+                       "alr",
+                       "embb",
+                       "gid",
+                       "katg",
+                       "pnca",
+                       "rpob"
+                     ),
+                     selected="embb"),
+                   menuItem("LogoP ED", tabName="LogoP ED"),
+                   
+                   sliderInput(
+                     "display_position_full_range"
+                     , "Display Positions"
+                     , min=1, max=150, value=c(1,150)
                    ),
-                   selected="embb"),
-                 menuItem("LogoP ED", tabName="LogoP ED"),
-                 
-                 sliderInput(
-                   "display_position_full_range"
-                   , "Display Positions"
-                   , min=1, max=150, value=c(1,150)
-                 ),
-                 
-                 conditionalPanel(
-                   condition="
+                   
+                   conditionalPanel(
+                     condition="
                                   input.sidebar == 'LogoP SNP' ||
                                   input.sidebar == 'LogoP OR' ||
                                   input.sidebar == 'LogoP ED'", 
-                   selectInput(
-                     "logoplot_colour_scheme", 
-                     label="Logo Plot Colour Scheme", 
-                     choices = logoPlotSchemes, 
-                     selected="chemistry"
+                     selectInput(
+                       "logoplot_colour_scheme", 
+                       label="Logo Plot Colour Scheme", 
+                       choices = logoPlotSchemes, 
+                       selected="chemistry"
+                     )
                    )
-                 )
-    )
-  ),
-  body <- dashboardBody(
-    
-    tabItems(
-      tabItem(tabName = "dashboard",
-              h2("Dashboard tab content")
-      ),
-      
-      tabItem(tabName = "widgets",
-              h2("Widgets tab content")
       )
     ),
-    # creates a 'Conditional Panel' containing a plot object from each of our 
-    # ggplot plot functions (and its associated data frame)
-    fluidRow(
-      column(
-        width=12,
-        plotOutput("LogoPlotMSA",
-                   click = "plot_click") %>% withSpinner(color="#0dc5c1")
+    body <- dashboardBody(
+      
+      tabItems(
+        tabItem(tabName = "dashboard",
+                h2("Dashboard tab content")
+        ),
+        
+        tabItem(tabName = "widgets",
+                h2("Widgets tab content")
+        )
+      ),
+      # creates a 'Conditional Panel' containing a plot object from each of our 
+      # ggplot plot functions (and its associated data frame)
+      fluidRow(
+        column(
+          width=12,
+          plotOutput("LogoPlotMSA",
+                     click = "plot_click") %>% withSpinner(color="#0dc5c1")
+        )
       )
     )
   )
-)
-#### Shiny Backend Server #####
-server <- function(input, output, session) {
-  observeEvent(
-    {
-      input$display_position_full_range #special-purpose for MSA
-      input$logoplot_colour_scheme
-      input$switch_target
-    },
-    {
-      # C O M P A T I B I L I T Y
-      #gene=input$switch_target
-      #drug=target_map[[gene]]
-      merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
-      
-      position_max=max(merged_df3[['position']])
-      position_min=min(merged_df3[['position']])
-      min_ligand_distance=min(merged_df3$ligand_distance)
-      max_ligand_distance=max(merged_df3$ligand_distance)
-      # FIXME: these are IMPORTANT
-      # # add "pos_count" position count column
-      # merged_df3=merged_df3 %>% dplyr::add_count(position)
-      # merged_df3$pos_count=merged_df3$n
-      # merged_df3$n=NULL
-      # 
-      mutable_df3 = cbind(merged_df3)
-      unified_msa = get(paste0(input$switch_target, '_unified_msa'))
-      # 
-      # # re-sort the dataframe according to position count
-      sorted_df = cbind(merged_df3)
-      sorted_df = sorted_df %>% arrange(pos_count)
-      
-      # 
-      outdir = paste0("~/git/Data/", drug, '/output/')
-      indir  = paste0("~/git/Data/", drug , "/input/")
-      # 
-      # source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary...
-      
-      #  source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
-      
-      #### nasty special-purpose merged_df3 variants ####
-      # FIXME: SLOW
-      # corr_plotdf = corr_data_extract(
-      #   merged_df3
-      #   , gene = gene
-      #   , drug = drug
-      #   , extract_scaled_cols = F
-      # )
-      
-      #input$stability_snp_param
-      
-      updateSliderInput(
-        session, 
-        "display_position_range",
-        min = position_min,
-        max = position_max
-        #, value = c(position_min, position_min+150)
-      )
-      updateSliderInput(
-        session,
-        "display_position_full_range",
-        min = 1, 
-        max = position_max #, 
-        # value = c(position_min, position_min+150)
-      )
-      updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min)
-      updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min)
-      updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance)
-      
-      stability_colname      = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
-      outcome_colname        = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
-      
-      display_position_range = input$display_position_range
-      plot_min=display_position_range[1]
-      plot_max=display_position_range[2]
-      
-      display_position_full_range = input$display_position_full_range
-      full_range_min=display_position_full_range[1]
-      full_range_max=display_position_full_range[2]
-      
-      logoplot_colour_scheme = input$logoplot_colour_scheme
-      omit_snp_count = input$omit_snp_count
-      
-      print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max))
-      
-      subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
-      
-      subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
-      subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),]
-      
-      
-      
-      #### LogoPlotMSA/Logo Plot ED ####
-      output$LogoPlotMSA = renderPlot(
-        LogoPlotMSA(target=input$switch_target,
-                    plot_positions=full_range_min:full_range_max,
-                    my_logo_col = logoplot_colour_scheme,
-                    aa_pos_drug = aa_pos_drug,
-                    active_aa_pos = active_aa_pos,
-                    aa_pos_lig1 = aa_pos_lig1,
-                    aa_pos_lig2 = aa_pos_lig2,
-                    aa_pos_lig3 = aa_pos_lig3
+  #### Shiny Backend Server #####
+  server <- function(input, output, session) {
+    observeEvent(
+      {
+        input$display_position_full_range #special-purpose for MSA
+        input$logoplot_colour_scheme
+        input$switch_target
+      },
+      {
+        # C O M P A T I B I L I T Y
+        #gene=input$switch_target
+        #drug=target_map[[gene]]
+        merged_df3=cbind(get(paste0(input$switch_target, '_merged_df3')))
+        
+        position_max=max(merged_df3[['position']])
+        position_min=min(merged_df3[['position']])
+        min_ligand_distance=min(merged_df3$ligand_distance)
+        max_ligand_distance=max(merged_df3$ligand_distance)
+        # FIXME: these are IMPORTANT
+        # # add "pos_count" position count column
+        # merged_df3=merged_df3 %>% dplyr::add_count(position)
+        # merged_df3$pos_count=merged_df3$n
+        # merged_df3$n=NULL
+        # 
+        mutable_df3 = cbind(merged_df3)
+        unified_msa = get(paste0(input$switch_target, '_unified_msa'))
+        # 
+        # # re-sort the dataframe according to position count
+        sorted_df = cbind(merged_df3)
+        sorted_df = sorted_df %>% arrange(pos_count)
+        
+        # 
+        outdir = paste0("~/git/Data/", drug, '/output/')
+        indir  = paste0("~/git/Data/", drug , "/input/")
+        # 
+        # source("~/git/LSHTM_analysis/scripts/plotting/logo_data_msa.R") # probably unnecessary...
+        
+        #  source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
+        
+        #### nasty special-purpose merged_df3 variants ####
+        # FIXME: SLOW
+        # corr_plotdf = corr_data_extract(
+        #   merged_df3
+        #   , gene = gene
+        #   , drug = drug
+        #   , extract_scaled_cols = F
+        # )
+        
+        #input$stability_snp_param
+        
+        updateSliderInput(
+          session, 
+          "display_position_range",
+          min = position_min,
+          max = position_max
+          #, value = c(position_min, position_min+150)
         )
-      )
-    }
-  )
-  
-  #### EOF Shiny Server ####
+        updateSliderInput(
+          session,
+          "display_position_full_range",
+          min = 1, 
+          max = position_max #, 
+          # value = c(position_min, position_min+150)
+        )
+        updateNumericInput(session, "selected_logop_snp_position", min = position_min, max = position_max, value = position_min)
+        updateNumericInput(session, "selected_logop_ed_position", min = position_min, max = position_max, value = position_min)
+        updateNumericInput(session, "corr_lig_dist", min = min_ligand_distance, max = max_ligand_distance, value = min_ligand_distance)
+        
+        stability_colname      = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
+        outcome_colname        = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
+        
+        display_position_range = input$display_position_range
+        plot_min=display_position_range[1]
+        plot_max=display_position_range[2]
+        
+        display_position_full_range = input$display_position_full_range
+        full_range_min=display_position_full_range[1]
+        full_range_max=display_position_full_range[2]
+        
+        logoplot_colour_scheme = input$logoplot_colour_scheme
+        omit_snp_count = input$omit_snp_count
+        
+        print(paste0('Plotting positions between: ', plot_min, ' and ', plot_max))
+        
+        subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
+        
+        subset_mutable_df3=mutable_df3[(mutable_df3$position>=plot_min & mutable_df3$position <=plot_max),]
+        subset_sorted_df=sorted_df[(sorted_df$position>=plot_min & sorted_df$position <=plot_max),]
+        
+        
+        
+        #### LogoPlotMSA/Logo Plot ED ####
+        output$LogoPlotMSA = renderPlot(
+          LogoPlotMSA(target=input$switch_target,
+                      plot_positions=full_range_min:full_range_max,
+                      my_logo_col = logoplot_colour_scheme,
+                      aa_pos_drug = aa_pos_drug,
+                      active_aa_pos = active_aa_pos,
+                      aa_pos_lig1 = aa_pos_lig1,
+                      aa_pos_lig2 = aa_pos_lig2,
+                      aa_pos_lig3 = aa_pos_lig3
+          )
+        )
+      }
+    )
+    
+    #### EOF Shiny Server ####
+    
+    
+    
+  }
+  ################ Running Server ##############
+  app <- shinyApp(ui, server)
   
   
-  
-}
-################ Running Server ##############
-app <- shinyApp(ui, server)
-
-
-runApp(app)
+  runApp(app)
 }
\ No newline at end of file