Merge pull request #42 from UMCUGenetics/dev

DIMSv2.1.0

.gitignore

@@ -9,3 +9,7 @@ GUI/src/config.R
 post/input
 post/output
 post/results
+
+#Macfiles
+.DS_Store
+pipeline/.DS_Store

GUI/src/config_default.R

@@ -14,6 +14,7 @@ db2 <- paste0(base, "/tools/db/HMDB_with_info_relevance_IS_C5OH.RData")
 
 ### Default parameters - for lists it defaults to the first one
 run_pipeline <- TRUE  # put on FALSE if you solely want to upload data
+
 # Everything below here doesn't need to be edited for every run, 
 # as the parameters in the GUI override these
 login <- ""
@@ -47,5 +48,32 @@ ssh_transfer <- "hpct01.op.umcutrecht.nl"
 commit <- paste(system("git name-rev HEAD", intern = TRUE), 
                 system("git rev-parse HEAD", intern = TRUE))
 
-
-# TODO Default job times
+### Max allowed time and memory per queued job 
+jobs <- list(
+  job_0 = list(time = "00:05:00", mem = "2G"),
+  job_1 = list(time = "00:05:00", mem = "2G"), 
+  job_2 = list(time = "00:10:00", mem = "4G"), 
+  job_3 = list(time = "01:30:00", mem = "5G"), 
+  job_4 = list(time = "01:00:00", mem = "8G"), 
+  job_5 = list(time = "02:00:00", mem = "8G"), 
+  job_6 = list(time = "02:30:00", mem = "4G"), 
+  job_7 = list(time = "01:00:00", mem = "8G"), 
+  job_8 = list(time = "01:00:00", mem = "8G"), 
+  job_9a = list(time = "00:30:00", mem = "4G"), 
+  job_9b = list(time = "00:30:00", mem = "4G"), 
+  job_10 = list(time = "01:00:00", mem = "8G"), 
+  job_11 = list(time = "03:00:00", mem = "8G"), 
+  job_12 = list(time = "00:30:00", mem = "8G"), 
+  job_13 = list(time = "01:00:00", mem = "8G"), 
+  job_14 = list(time = "00:05:00", mem = "500M"),
+  job_hmdb1 = list(time = "03:00:00", mem = "8G"),
+  job_hmdb2 = list(time = "03:00:00", mem = "8G"),
+
+  queue_0 = list(time = "00:05:00", mem = "1G"), 
+  queue_1 = list(time = "00:05:00", mem = "1G"), 
+  queue_2 = list(time = "00:05:00", mem = "500M"), 
+  queue_3 = list(time = "00:05:00", mem = "500M"), 
+  queue_4 = list(time = "00:05:00", mem = "500M"), 
+  queue_5 = list(time = "00:05:00", mem = "500M"), 
+  queue_6 = list(time = "00:05:00", mem = "500M")
+)

GUI/src/server.R

@@ -104,10 +104,15 @@ function(input, output, session) {
     t_reps <- trimws(selected_samples[,1]) # technical replicates / samples, usually 3 per biological replicate
     b_reps <- trimws(selected_samples[,2]) # biological replicates / patients
     wrong_t_rep_count = FALSE
+    wrong_samplenames = c()
     for (b_rep in unique(b_reps)) {
       if (sum(b_reps == b_rep) != input$nrepl) {
         wrong_t_rep_count = TRUE
       }
+      # check 10 : if name fits requirements ( + -> 1 or more, * -> 0 or more)
+      if (grepl("^(?:(?!(C|P))[a-zA-Z0-9]+_{1})?(C|P){1}[0-9]+\\.([1-9]\\d*)+", b_rep, perl = TRUE) != TRUE) {
+        wrong_samplenames <- c(b_rep, wrong_samplenames)
+      }
     }
     if (length(t_reps) == 0 || wrong_t_rep_count || length(t_reps) / input$nrepl != length(unique(b_reps))) {
       output$check4 <- renderText({"No"})
@@ -116,6 +121,18 @@ function(input, output, session) {
       output$check4 <- renderText({"Yes"})
     }
 
+    # check 10 continued
+    if (input$z_score == "1") {
+      if (length(wrong_samplenames) > 0) {
+        output$check10 <- renderText({"No"})
+        output$check10_extra <- renderText({paste0("Wrong: ", paste(wrong_samplenames, collapse=', '))})
+        passed = FALSE
+      } else {
+        output$check10 <- renderText({"Yes"})
+        output$check10_extra <- renderText({""})
+      }
+    }
+
     # check 5 : Parameters 
     if (input$login == '' ||
         input$password == '' ||
@@ -240,6 +257,11 @@ function(input, output, session) {
       paste0("db2=", config$db2)
     )
 
+    for (i in 1:length(config$jobs)) {
+      parameters <- c(parameters, paste0(names(config$jobs)[[i]], "_time=", config$jobs[[i]]$time))
+      parameters <- c(parameters, paste0(names(config$jobs)[[i]], "_mem=", config$jobs[[i]]$mem))
+    }
+
     writeLines(parameters, file_con, sep = "\n")
     close(file_con)
 
@@ -258,10 +280,10 @@ function(input, output, session) {
     ### Transfer over RAW data
     input_folder_name <- paste(as.vector(unlist(input$input_folder['path']))[-1], collapse = "/", sep="")
     input_dir = paste(config$root, input_folder_name, sep = "/")
+    raw_files <- paste0(input_dir, "/", t_reps, ".raw")
     cat("Copying files from", input_dir, "to:", hpc_input_dir, "... (ignore the %)\n")
-
     scp_upload(ssh_transfer, 
-               list.files(path = input_dir, pattern = ".raw$", full.names = TRUE), 
+               raw_files, 
                to = hpc_input_dir)
 
     ### Transfer over the tmp files to raw data folder (init.RData, settings.config)

GUI/src/ui.R

@@ -90,6 +90,11 @@ dashboardPage(
                 column(1, textOutput("check4")),
                 column(11, p(tags$b("Every biological sample has the correct amount of technical replicates."))),
                 br(),br(),
+                column(1, textOutput("check10")),
+                column(11, p(tags$b("If Z score enabled, all biological samples follow the naming requirements (must contain C or P, etc.)"))),
+                column(1),
+                column(11, textOutput("check10_extra")),
+                br(),br(),
                 column(1, textOutput("check5")),
                 column(11, p(tags$b("All parameters have been filled in and selected."))),
                 br(),br(),