X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fscripts%2Frb_dir_qsub.rb;h=fffafce82b97ae652e4b068d9677d49cce121c08;hb=8f9465b50e205b87c7a01c65c859309293aee085;hp=c2749bb347a2ba58f0c235fd603110a2f4f41422;hpb=253a714c2440558d7c70fe30cac5d7b093798968;p=jalview.git

diff --git a/forester/ruby/scripts/rb_dir_qsub.rb b/forester/ruby/scripts/rb_dir_qsub.rb
index c2749bb..fffafce 100644
--- a/forester/ruby/scripts/rb_dir_qsub.rb
+++ b/forester/ruby/scripts/rb_dir_qsub.rb
@@ -30,130 +30,136 @@
 
 module ForesterScripts
 
-    if RUBY_VERSION !~ /1.9/
-        puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
-        exit( -1 )
-    end
+  if RUBY_VERSION !~ /1.9/
+    puts( "Your ruby version is #{RUBY_VERSION}, expected 1.9.x " )
+    exit( -1 )
+  end
 
-    PARAMETER_FILE = 'parameters.rb_dir_qsub'
-    SLEEP          = 1.0
-    REMOVE_SUFFIX  = true
+  PARAMETER_FILE = 'parameters.rb_dir_qsub'
+  SLEEP          = 1.0
+  REMOVE_SUFFIX  = true
+  LIMIT_TO_TAX_CODE  = true
 
-    PRG         = 'PRG:'
-    OPT         = 'OPT:'
-    VOPT        = 'VOPT:'
-    OUTPUT_OPT  = 'OUTPUT:'
-    SUFFIX      = 'SUFFIX:'
-    INPUT_PART  = 'INPUT_PART:'
+  PRG         = 'PRG:'
+  OPT         = 'OPT:'
+  VOPT        = 'VOPT:'
+  OUTPUT_OPT  = 'OUTPUT:'
+  SUFFIX      = 'SUFFIX:'
+  INPUT_PART  = 'INPUT_PART:'
 
 
-    PBS_O_WORKDIR       = '$PBS_O_WORKDIR/'
-    TMP_CMD_FILE_SUFFIX = '__QSUB'
-    NAME                = 'rb_dir_qsub'
+  PBS_O_WORKDIR       = '$PBS_O_WORKDIR/'
+  TMP_CMD_FILE_SUFFIX = '__QSUB'
+  NAME                = 'rb_dir_qsub'
 
-    if ( !File.exists?( PARAMETER_FILE ) )
-        puts( '[' + NAME + '] > parameters file "' + PARAMETER_FILE + '" not found' )
-        Process.exit!
-    end
-    puts( '[' + NAME + '] > reading ' + PARAMETER_FILE )
+  if ( !File.exists?( PARAMETER_FILE ) )
+    puts( '[' + NAME + '] > parameters file "' + PARAMETER_FILE + '" not found' )
+    Process.exit!
+  end
+  puts( '[' + NAME + '] > reading ' + PARAMETER_FILE )
 
-    prg = ''
-    opt = ''
-    vopts = Array.new
-    suffix = ''
-    input_part = ''
-    output_opt = ''
-    open( PARAMETER_FILE ).each { |line|
-        if ( line.length > 1 && line =~ /^[^#]\S+/ )
-            if line =~ /^#{PRG}\s+(\S+)/
-                prg = $1
-            end
-            if line =~ /^\s*#{OPT}\s+(\S+.+)/
-                opt = $1
-            end
-            if line =~ /^\s*#{VOPT}\s+(\S+.+)/
-                vopts.push( $1 )
-            end
-            if line =~ /^\s*#{SUFFIX}\s+(\S+)/
-                suffix = $1
-            end
-            if line =~ /^\s*#{INPUT_PART}\s+(\S+)/
-                input_part = $1
-            end
-            if line =~ /^\s*#{OUTPUT_OPT}\s+(\S+.+)/
-                output_opt = $1
-            end
-        end
-    }
-    if ( prg.length < 1 )
-        puts( '[' + NAME + '] > no program name found in parameters file "' + PARAMETER_FILE + '"' )
-        Process.exit!
-    end
-    puts( '[' + NAME + '] > program: ' + prg )
-    puts( '[' + NAME + '] > option :  ' + opt )
-    vopts.each { |vopt|
-        puts( '[' + NAME + '] > voption:  ' + vopt )
-    }
-    puts( '[' + NAME + '] > suffix :  ' + suffix )
-    if ( input_part.length > 0 )
-        puts( '[' + NAME + '] > input:  ' + input_part )
-    end
-    if ( output_opt.length > 0 )
-        puts( '[' + NAME + '] > output opt :  ' + output_opt )
-    end
-    if vopts.empty?
-        vopts.push( "" )
+  prg = ''
+  opt = ''
+  vopts = Array.new
+  suffix = ''
+  input_part = ''
+  output_opt = ''
+  open( PARAMETER_FILE ).each { |line|
+    if ( line.length > 1 && line =~ /^[^#]\S+/ )
+      if line =~ /^#{PRG}\s+(\S+)/
+        prg = $1
+      end
+      if line =~ /^\s*#{OPT}\s+(\S+.+)/
+        opt = $1
+      end
+      if line =~ /^\s*#{VOPT}\s+(\S+.+)/
+        vopts.push( $1 )
+      end
+      if line =~ /^\s*#{SUFFIX}\s+(\S+)/
+        suffix = $1
+      end
+      if line =~ /^\s*#{INPUT_PART}\s+(\S+)/
+        input_part = $1
+      end
+      if line =~ /^\s*#{OUTPUT_OPT}\s+(\S+.+)/
+        output_opt = $1
+      end
     end
+  }
+  if ( prg.length < 1 )
+    puts( '[' + NAME + '] > no program name found in parameters file "' + PARAMETER_FILE + '"' )
+    Process.exit!
+  end
+  puts( '[' + NAME + '] > program: ' + prg )
+  puts( '[' + NAME + '] > option :  ' + opt )
+  vopts.each { |vopt|
+    puts( '[' + NAME + '] > voption:  ' + vopt )
+  }
+  puts( '[' + NAME + '] > suffix :  ' + suffix )
+  if ( input_part.length > 0 )
+    puts( '[' + NAME + '] > input:  ' + input_part )
+  end
+  if ( output_opt.length > 0 )
+    puts( '[' + NAME + '] > output opt :  ' + output_opt )
+  end
+  if vopts.empty?
+    vopts.push( "" )
+  end
 
-    files = Dir.entries( "." )
+  files = Dir.entries( "." )
 
-    files.each { |file|
-        if ( !File.directory?( file ) && file !~ /^\./ && file !~ /#{PARAMETER_FILE}/ )
+  files.each { |file|
+    if ( !File.directory?( file ) && file !~ /^\./ && file !~ /#{PARAMETER_FILE}/ )
 
-            if ( input_part.length > 0 && file !~ /#{input_part}/ )
-                next
-            end
-            vopts.each { |vopt|
-                cmd = ""
-                outputfile = file.to_str
-                if REMOVE_SUFFIX
-                    if outputfile =~ /(.+)\..{1,5}/
-                        outputfile = $1
-                    end
-                end
-                if output_opt.length > 0
-                    cmd = prg + ' ' +
-                     output_opt + ' ' + PBS_O_WORKDIR + outputfile + suffix + ' ' +
-                     opt + ' ' +
-                     PBS_O_WORKDIR + file.to_str +
-                     ' > /dev/null'
-                elsif vopt.length > 0
-                    cmd = prg + ' ' + opt + ' ' + vopt + ' ' + PBS_O_WORKDIR + file.to_str +
-                     ' > ' + PBS_O_WORKDIR + vopt + "_" + outputfile + suffix
-                else
-                    cmd = prg + ' ' + opt + ' ' + PBS_O_WORKDIR + file.to_str +
-                     ' > ' + PBS_O_WORKDIR + outputfile + suffix
-                end
-                tmp_cmd_file = file.to_str + TMP_CMD_FILE_SUFFIX
-                if File.exists?( tmp_cmd_file )
-                    File.delete( tmp_cmd_file )
-                end
-                open( tmp_cmd_file, 'w' ) do |f|
-                    f.write( cmd )
-                end
-                puts( '[' + NAME + '] > excuting ' + cmd )
-                IO.popen( 'qsub ' + tmp_cmd_file , 'r+' ) do |pipe|
-                    pipe.close_write
-                    puts pipe.read
-                end
-                sleep( SLEEP )
-                if File.exists?( tmp_cmd_file )
-                    File.delete( tmp_cmd_file )
-                end
-            }
+      if ( input_part.length > 0 && file !~ /#{input_part}/ )
+        next
+      end
+      vopts.each { |vopt|
+        cmd = ""
+        outputfile = file.to_str
+        if LIMIT_TO_TAX_CODE
+          if outputfile =~ /^([A-Z0-9]{3,5})[_\.]/
+            outputfile = $1
+          end
+        end
+        if REMOVE_SUFFIX
+          if outputfile =~ /(.+)\..{1,5}/
+            outputfile = $1
+          end
         end
-    }
-    puts( '[' + NAME + '] > OK.' )
-    puts
+        if output_opt.length > 0
+          cmd = prg + ' ' +
+           output_opt + ' ' + PBS_O_WORKDIR + outputfile + suffix + ' ' +
+           opt + ' ' +
+           PBS_O_WORKDIR + file.to_str +
+           ' > /dev/null'
+        elsif vopt.length > 0
+          cmd = prg + ' ' + opt + ' ' + vopt + ' ' + PBS_O_WORKDIR + file.to_str +
+           ' > ' + PBS_O_WORKDIR + vopt + "_" + outputfile + suffix
+        else
+          cmd = prg + ' ' + opt + ' ' + PBS_O_WORKDIR + file.to_str +
+           ' > ' + PBS_O_WORKDIR + outputfile + suffix
+        end
+        tmp_cmd_file = file.to_str + TMP_CMD_FILE_SUFFIX
+        if File.exists?( tmp_cmd_file )
+          File.delete( tmp_cmd_file )
+        end
+        open( tmp_cmd_file, 'w' ) do |f|
+          f.write( cmd )
+        end
+        puts( '[' + NAME + '] > excuting ' + cmd )
+        IO.popen( 'qsub ' + tmp_cmd_file , 'r+' ) do |pipe|
+          pipe.close_write
+          puts pipe.read
+        end
+        sleep( SLEEP )
+        if File.exists?( tmp_cmd_file )
+          File.delete( tmp_cmd_file )
+        end
+      }
+    end
+  }
+  puts( '[' + NAME + '] > OK.' )
+  puts
 
 end