Replace jobs.bch with annotation_jobs.bch

Author: marinak-ebi

Late adults stats pipeline/DRrequiredAgeing/DRrequiredAgeingPackage/R/sideFunctions.R

@@ -5128,7 +5128,7 @@ IMPC_annotationPostProcess = function(SP.results = getwd(),
   system('split -15000 AllResultsIndeces.txt split_index_', wait = TRUE)
 
 
-  system('rm -f jobs.bch', wait = TRUE)
+  system('rm -f annotation_jobs.bch', wait = TRUE)
   system('rm -f config.Rdata', wait = TRUE)
   system('rm -f logs.zip' , wait = TRUE)
   system('rm -f loader.R', wait = TRUE)
@@ -5145,9 +5145,9 @@ IMPC_annotationPostProcess = function(SP.results = getwd(),
     pattern = 'split_index',
     mem = "12G",
     time = "2-00",
-    outputfile = 'jobs.bch'
+    outputfile = 'annotation_jobs.bch'
   )
-  system('chmod 775 jobs.bch', wait = TRUE)
+  system('chmod 775 annotation_jobs.bch', wait = TRUE)
 
 
   if (is.null(mp_chooser_file) || !file.exists(file.path(DRrequiredAgeing:::local(), 'annotation', mp_chooser_file))) {
@@ -5168,7 +5168,7 @@ IMPC_annotationPostProcess = function(SP.results = getwd(),
     wait = TRUE
   )
 
-  system('sbatch --job-name=impc_stats_pipeline_job --time=01:00:00 --mem=1G -o ../annotation_postprocess_job_id.txt --wrap="bash ./jobs.bch"', wait = TRUE)
+  system('sbatch --job-name=impc_stats_pipeline_job --time=01:00:00 --mem=1G -o ../annotation_postprocess_job_id.txt --wrap="bash ./annotation_jobs.bch"', wait = TRUE)
   DRrequiredAgeing:::waitTillCommandFinish(
     WaitIfTheOutputContains = waitUntillSee,
     ignoreline = ignoreThisLineInWaitingCheck
@@ -6318,7 +6318,7 @@ annotationIndexCreator = function(path = getwd(),
                                   pattern = 'split_index',
                                   mem = "12G",
                                   time = "2-00",
-                                  outputfile = 'jobs.bch') {
+                                  outputfile = 'annotation_jobs.bch') {
   lf = list.files(
     path = path,
     pattern = pattern,
@@ -6488,7 +6488,7 @@ IMPC_HadoopLoad = function(SP.results = getwd(),
   system('split -50 AllResultsIndeces.txt split_index_', wait = TRUE)
 
 
-  system('rm -f jobs.bch', wait = TRUE)
+  system('rm -f annotation_jobs.bch', wait = TRUE)
   system('rm -f config.Rdata', wait = TRUE)
   system('rm -f configHadoop.Rdata', wait = TRUE)
   system('rm -f logs.zip' , wait = TRUE)
@@ -6506,9 +6506,9 @@ IMPC_HadoopLoad = function(SP.results = getwd(),
     pattern = 'split_index',
     mem = "5G",
     time = "2-00",
-    outputfile = 'jobs.bch'
+    outputfile = 'annotation_jobs.bch'
   )
-  system('chmod 775 jobs.bch', wait = TRUE)
+  system('chmod 775 annotation_jobs.bch', wait = TRUE)
 
 
   if (is.null(mp_chooser_file) || !file.exists(file.path(DRrequiredAgeing:::local(), 'annotation', mp_chooser_file))) {
@@ -6529,7 +6529,7 @@ IMPC_HadoopLoad = function(SP.results = getwd(),
     wait = TRUE
   )
 
-  submit_limit_jobs(bch_file="jobs.bch", job_id_logfile="../../../../compressed_logs/hadoop_load_job_id.txt")
+  submit_limit_jobs(bch_file="annotation_jobs.bch", job_id_logfile="../../../../compressed_logs/hadoop_load_job_id.txt")
   DRrequiredAgeing:::waitTillCommandFinish(
     WaitIfTheOutputContains = waitUntillSee,
     ignoreline = ignoreThisLineInWaitingCheck