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
git://source.jalview.org / jalview.git / blobdiff