Icarus Class: Application
Description of an application to be called on data of a certain type. This includes its name, a description of the application, command line options for that application, and other related attributes. This description should normally take place in $SRSDB directory. Defining a new application requires few steps and should be checked from srs administrator manual.
name Attribute may stay unnamed in attribute list.Attribute value must be specified.
  Name of the application.
printName  
  Print name of the application.
package Package  
groups Attribute is multivalued (list). ApplGroup  
  Application group(s) the application belongs to
category  
  Category of the application.
supplier  
  Supplier of the application.
version  
  Version of the application required for this definition.
installation  
  Installation of the application.
comment  
  Comment is used in building application information page, which is available through srs web interface.
title  
  Short description of the program, which can be used in a title line.
helpUrl  
  URL of help page.
iFile  
  Name of the .i file.
options Attribute is multivalued (list). AppOpt  
  List of command line options.
parameterSetList Attribute is multivalued (list). ApplParameterSet  
  List of pre-defined parameter sets for the current application.
validationRules Attribute is multivalued (list). ValidationRule  
  Validation rules for the application options.
resultDb Library Attribute value must be specified.
  Result databank.
command  
  Icarus script used to define the command line to call the application program.
commandWrapper  
  This is an optional argument and exists if there should be some pre/post commands before or after the actual launch command. If the application requires pre/post processing, place the related lines before/after '$opt.command' line. When there is an explicit language described by the first line then the language is used to execute the wrapper, otherwise csh is used by default.
resultUrl  
  Icarus script to generate the URL of the result page. The result of the last expression will be used as resultURL. This could be useful to make the result file available when we do not have a parser for an application. example: wgetz?-id+$ParStr:userId+-page+jobDebug+-jobName+blastp/$appl.outFile In this example the result file is in an application specific directory.
resultQuery  
  Icarus script to generate the query to retrieve result entry(s). The result of the last expression will be used as resultQuery.
launchFromTopPage  
  Use one of the following values. y n
  If y then allow the application to be launched from the top page.
launchFromResultPages  Attribute has a default value. y
  Use one of the following values. y n
  If n then only allow the application to be launched from the applications page.
parallelJobs  Attribute has a default value. n
  Use one of the following values. y n
  If yes then each input sequence is submitted as separate jobs.
restrictTo Attribute is multivalued (list). User  
  Restrict access to the users listed.
estimatedRunTime  
  Estimated run time for the application, in seconds.
specPattern  
  specific pattern may occur in the output file.
minFileSize  
  Minimum file size for a valid result.
minLines  
  Minimum number of lines in the output file for a valid result.
dependencies Attribute is multivalued (list). Dependency  
  Parameter dependencies for the application.
removeOnExit  Attribute has a default value. no
  Use one of the following values. y n yes no
  Delete application scripts after an application job is completed. This might be useful for having less files in session directories.
launchNow
Launches an srs application. If the syncLaunch option is 'true' then the job is virtually synchronus even if it is submitted to a batch queue system.
syncLaunch Argument has a default value. false 
Use one of the following values. true false
Returns a value
optFile
Returns the file name used to create a temporary file containing the option's value. This temporary file typically serves as input for the application.
opt Argument may stayunnamed in argument list.Argument must be specified. 
Returns a value
optseq
Returns the sequence as a string for a sequence input option. Intended for sequence input AppOpts but may have general use. The option name defaults to 'in', the usual name for the input sequence.
opt Argument may stayunnamed in argument list.Argument has a default value. in 
Application option name (default is 'in')
seqn  
Sequence number in a list or set
Returns a value
optseqlen
Returns the length of a sequence for a sequence input option. Applicable to sequence input AppOpts only. The option name defaults to 'in', the usual name for the input sequence.
opt Argument may stayunnamed in argument list.Argument has a default value. in 
Application option name (default is 'in')
seqn  
Sequence number in a list or set
Returns a value
optseqtype
Returns the type of a sequence for a sequence input option. Applicable to sequence input AppOpts only. The option name defaults to 'in', the usual name for the input sequence.
opt Argument may stayunnamed in argument list.Argument has a default value. in 
Application option name (default is 'in')
seqn  
Sequence number in a list or set
Returns a value
optsize
Returns the number of elements in the option value. Intended for sequence input AppOpts but may have general use. The option name defaults to 'in', the usual name for the input sequence.
opt Argument may stayunnamed in argument list.Argument has a default value. in 
Application option name (default is 'in')
Returns a value
outFile
Returns a name that can be used for the output file generated by the application.
name Argument may stayunnamed in argument list.Argument has a default value. tmp 
Returns a value