Fix workflows

R/helper_functions.R

@@ -107,7 +107,7 @@ getInstallToolPackageWorkflow <- function(tool, containerType) {
   size <- length(data)
   
   intalls <- ""
-  res <- ""
+  res <- c()
   
   for (tools in data) {
     splitB <- strsplit(tool, "%")  
@@ -118,11 +118,10 @@ getInstallToolPackageWorkflow <- function(tool, containerType) {
       if(tools$version == version) {
         for (c in tools$dependencies) {
           tt <- paste0(c$name, "%", c$version)
-          print(tt)
-          res <- paste0(res, getInstallToolPackageBioContainer(tt, containerType))
-          res <- paste0(res, "\n")
+          res <- c(res, getInstallToolPackageBioContainer(tt, containerType))
         }
-        res <- paste0(res, "\t", tools$install, collapse='\n' )
+        res <- c(res, paste0("\t", tools$install, collapse='\n' ))
+        print(res)
         return(res)
       }
     }

server/opt_home.R

@@ -517,13 +517,16 @@ createWorkflows <- function(result, haveR, haveConda) {
     
     for (tool in selectWorkflows){
       
-      result <- paste(result, '############### Install Workflow tools ##############', sep = "\n")
+      result <- paste(result, '############### Install Workflow tools ##############\n', sep = "\n")
       
       
-      result <- paste(result, getInstallToolPackageWorkflow(tool, input$containerType), sep="\n\n")
+      for(i in getInstallToolPackageWorkflow(tool, input$containerType)) {
+        result <- paste0(result, i, "\n")
+      }
+      
     }
   } else {
-    selectBioTool <- input$selectedBiocontainer
+    selectWorkflows <- input$selectedWorkflows
     
     result <- paste0(result, "\n")
     
@@ -573,12 +576,13 @@ createWorkflows <- function(result, haveR, haveConda) {
     result <- paste(result, "RUN chmod 777 -R /opt/workflows/", sep = "\n")
     result <- paste(result, "ENV PATH=/opt/workflows/bin:${PATH}", sep = "\n")
     
-    for (tool in selectBioTool){
-      
-      result <- paste(result, '############### Install Workflow ##############', sep = "\n")
+    for (tool in selectWorkflows){
       
+      result <- paste(result, '############### Install Workflow ##############\n', sep = "\n")
       
-      result <- paste0(result, "\nRUN ", getInstallToolPackageWorkflow(tool, input$containerType))
+      for(i in getInstallToolPackageWorkflow(tool, input$containerType)) {
+        result <- paste0(result, "RUN", i, "\n")
+      }
     }
     
   }
@@ -635,7 +639,7 @@ createBiocontainer <- function(result, haveR) {
     
     for (tool in selectBioTool){
       
-      result <- paste(result, '############### Install BioContainer tools ##############', sep = "\n")
+      result <- paste(result, '############### Install BioContainer tools ##############\n', sep = "\n")
       
       
       result <- paste(result, getInstallToolPackageBioContainer(tool, input$containerType), sep="\n\n")
@@ -684,10 +688,10 @@ createBiocontainer <- function(result, haveR) {
     
     for (tool in selectBioTool){
       
-      result <- paste(result, '############### Install BioContainer tools ##############', sep = "\n")
+      result <- paste(result, '############### Install BioContainer tools ##############\n', sep = "\n")
       
       
-      result <- paste0(result, "\nRUN ", getInstallToolPackageBioContainer(tool, input$containerType))
+      result <- paste0(result, "RUN ", getInstallToolPackageBioContainer(tool, input$containerType))
     }
     
   }