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This page describe the distribution content and how to run each of the 3 availables modes, after briefly presenting them.

• Java version 1.6 or higher must be installed on your computer and the full path to the java.exe executable must be declared in your PATH. If not, you must modify the run*.bat script to specify the full path to the executable.
• Windows : as there is dlls required to parse mascot data, windows is mandatory
• 32/64bits : IRMa is made for 32bits système but since version 1.29.0 using it on 64bits systems is possible (but you will not have access to embedded browser so Protein mascot view, Peptide mascot view and Public database view will not be available ). To pass to 64bits mode :
  • open the install directory of IRMa
  • open the lib directory
  • rename msparserj.dll to msparserj32.dll
  • rename msparserj64.dll to msparserj.dll

To install IRMa you only have to unzip IRMa-<version>.zip file on your local system. Under the main directory, the following structure will ne available :

  > auto : directory containing script samples for the automatic or batch mode. 
  > db : SQL scripts to create an identification database or to migrate an existing one. 
         If the data model has been modified, the provided script will permit data recovery from an //old// identification databases 
  > lib : libs and dll needed by IRMa
  > VBscripts: Visual Basic scripts used to launch IRMa from Mascot Daemon. IRMa will be executed in automatic mode. 
  > IRMa-<version>.jar : IRMa library specific code
  > *.bat : batch to run IRMa in specific mode. See following sections.  

Run batch file run.bat.
A graphical interface will allow user to validate a Mascot identification result. Help on validation and others features is accessible in user guide.

Note
To validate big Mascot identification, it is possible to increase memory used by the application: Edit run.bat file and change the value parameter in -Xmx<value>m attribute. This value correspond to the amount of memory which will be allocated to IRMa, in Mo. Be careful to not specify a value equal (or upper!) to your PC memory full capacity !

Run batch file runBatch.bat.
This mode allow to execute a set of operations, in a automatic manner, on a set of Mascot identification results or on previously saved IRMa projects. Operations to be executed can be uploaded from a script file or can be edited in IRMa Batch interface.

A complete description of the use and configuration of IRMa Batch is available.

Attention runBatch.bat file is only a example of how to run IRMa in this mode.

The automatic mode allow to execute a set of operations, defined in a script file, on a specific Mascot identification result. The script file is the same as the one used in batch mode. See IRMa Batch documentation. This mode has no user interface.