lib/sushi_fabric/sushiApp.rb in sushi_fabric-0.2.8 vs lib/sushi_fabric/sushiApp.rb in sushi_fabric-0.3.1

@@ -1,8 +1,8 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20141009-135300'
+# Version = '20141202-095124'
 
 require 'csv'
 require 'fileutils'
 require 'yaml'
 require 'drb/drb'
@@ -315,14 +315,14 @@
 set -o pipefail
 
 #### SET THE STAGE
 SCRATCH_DIR=#{@scratch_dir}
 GSTORE_DIR=#{@gstore_dir}
-mkdir $SCRATCH_DIR || exit 1
-cd $SCRATCH_DIR || exit 1
 echo "Job runs on `hostname`"
 echo "at $SCRATCH_DIR"
+mkdir $SCRATCH_DIR || exit 1
+cd $SCRATCH_DIR || exit 1
 
     EOF
   end
   def job_footer
     @out.print "#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP\n"
@@ -409,27 +409,27 @@
         out << headers.map{|header| row_hash[header]}
       end
     end
     file_path
   end
-  def copy_commands(org_dir, dest_parent_dir)
-    @workflow_manager.copy_commands(org_dir, dest_parent_dir)
+  def copy_commands(org_dir, dest_parent_dir, now=nil)
+    @workflow_manager.copy_commands(org_dir, dest_parent_dir, now)
   end
   def copy_inputdataset_parameter_jobscripts
     org = @scratch_result_dir
     dest = @gstore_project_dir
-    copy_commands(org, dest).each do |command|
+    copy_commands(org, dest, 'now').each do |command|
       puts command
       unless system command
         raise "fails in copying input_dataset, parameters and jobscript files from /scratch to /gstore"
       end
     end
-    sleep 1
+    #sleep 1
   end
   def copy_nextdataset
     org = @next_dataset_tsv_path
     dest = File.join(@gstore_project_dir, @result_dir_base)
-    copy_commands(org, dest).each do |command|
+    copy_commands(org, dest, 'now').each do |command|
       puts command
       unless system command
         raise "fails in copying next_dataset files from /scratch to /gstore"
       end
     end