refit jobs with large counts files are now run via bsub. changing the…

… way permissions check for file modification is done

R/global.R

@@ -432,14 +432,18 @@ verify_access_to_write <- function(sample_path) {
 
   can_edit_review = F
   if (file.exists(review_file)) {
-    can_edit_review = !system(paste0('touch -a -r ', review_file, ' ', review_file), ignore.stderr = T)
+    #can_edit_review = !system(paste0('touch -a -r ', review_file, ' ', review_file), ignore.stderr = T)
+    can_edit_review = !system(paste0('(mv ', review_file, ' ', review_file, '. ; ', 
+                                     ' mv ', review_file, '. ', review_file, ') 2> /dev/null'), ignore.stderr = T)
   } else {
     can_edit_review = has_permissions_to_write(sample_path)
   }
 
   can_edit_qc = F
   if (file.exists(qc_file)) {
-    can_edit_qc = !system(paste0('touch -c -a -r ', qc_file, ' ', qc_file), ignore.stderr = T)
+    #can_edit_qc = !system(paste0('touch -c -a -r ', qc_file, ' ', qc_file), ignore.stderr = T)
+    can_edit_qc = !system(paste0('(mv ', qc_file, ' ', qc_file, '. ; ', 
+                                 ' mv ', qc_file, '. ', qc_file, ') 2> /dev/null'), ignore.stderr = T)
   } else {
     can_edit_qc = has_permissions_to_write(sample_path)
   }

example_facets_preview.json

@@ -31,6 +31,6 @@
   "verify_sshfs_mount" : "juno",
   "r_script_path" : "/opt/common/CentOS_7-dev/bin/Rscript",
   "facets_suite_lib": "/juno/work/ccs/shared/software/R_libs/facetsSuite/2.0.6/",
-  "facets_suite_run_wrapper": "/juno/work/ccs/shared/software/R_libs/facetsSuite/2.0.4/run-facets-wrapper.R",
+  "facets_suite_run_wrapper": "/juno/work/ccs/shared/software/R_libs/facetsSuite/2.0.6/run-facets-wrapper.R",
   "facets_qc_script": "/juno/work/ccs/bandlamc/git/facets-preview/facets_qc/v1.0/facets_fit_qc.R"
 }

inst/application/server.R

@@ -802,27 +802,35 @@ function(input, output, session) {
 
     name_tag = glue(name_tag)
     refit_name <- glue('/refit_{name_tag}')
+
     cmd_script_pfx = paste0(values$config$watcher_dir, "/refit_jobs/facets_refit_cmd_")
-    refit_cmd_file <- glue("{cmd_script_pfx}{sample_id}_{name_tag}.sh")
-
+
     refit_dir <- paste0(run_path, refit_name)
     facets_lib_path = supported_facets_versions[version==facets_version_to_use]$lib_path
+
     counts_file_name = glue("{run_path}/countsMerged____{sample_id}.dat.gz")
-
-    if (any(values$submitted_refit == refit_dir)) {
-      showModal(modalDialog(
-        title = "Not submitted", paste0("Job already queued. Check logs: ", refit_cmd_file, ".*")
-      ))
-      return(NULL)
-    }
-
     if (!is.null(values$selected_repo)) {
       counts_file_name = glue(paste0("{run_path}/",values$selected_repo$counts_file_format))
     }
 
     if (!file.exists(counts_file_name)) {
+      # try alternate counts file; tempo format; eg: SU2LC_MSK_1365_T__SU2LC_MSK_1365_N.snp_pileup.gz
+      if (file.exists(glue("{run_path}/{sample_id}.snp_pileup.gz"))) {
+        counts_file_name = glue("{run_path}/{sample_id}.snp_pileup.gz")
+      } else {
+        showModal(modalDialog( title = "Not submitted", paste0("Counts file does not exist: ", counts_file_name) ))
+        return(NULL)
+      }
+    }
+
+    refit_cmd_file <- glue("{cmd_script_pfx}{sample_id}_{name_tag}.sh")
+    if (file.size(counts_file_name) > 5e7) {
+      refit_cmd_file <- glue("{cmd_script_pfx}{sample_id}_{name_tag}.bsub.sh")  
+    }
+
+    if (any(values$submitted_refit == refit_dir)) {
       showModal(modalDialog(
-        title = "Not submitted", paste0("Counts file does not exist: ", counts_file_name)
+        title = "Not submitted", paste0("Job already queued. Check logs: ", refit_cmd_file, ".*")
       ))
       return(NULL)
     }

refit_watcher/refit_watcher.sh

@@ -4,8 +4,6 @@ WATCHER_DIR="/juno/work/ccs/shared/software/refit_watcher/"
 
 INOTIFY_SH="$WATCHER_DIR/bin/refit_watcher_inotify_cmd.sh"
 
-rm -f $INOTIFY_SH
-
 nohup sh -c "sleep 4; touch $WATCHER_DIR/refit_jobs/facets_refit_cmd_watcher_poll.sh" 2> /dev/null > /dev/null &
 
 echo "
@@ -16,6 +14,10 @@ $WATCHER_DIR/bin/inotifywait --format '%w%f' --include 'facets_refit_cmd_.*sh\$'
     if [[ \"\$FILE\" =~ \"facets_refit_cmd_watcher_poll.sh\" ]]; then
         echo \$CUR_TIME inotify is running
         nohup bash -c 'sleep 59; touch $WATCHER_DIR/refit_jobs/facets_refit_cmd_watcher_poll.sh' &
+    elif [[ \"\$FILE\" =~ \"bsub.sh\" ]]; then
+        echo \$CUR_TIME Running: \$FILE
+        bsub -We 1:59 -n 4 -R \"rusage[mem=16]\" -o \$FILE.log -e \$FILE.err bash \$FILE
+        echo \$CUR_TIME Finished: \$FILE
     else
         echo \$CUR_TIME Running: \$FILE
         bash \$FILE > \$FILE.log 2> \$FILE.err &