instalguide
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instalguide [2009/01/20 08:35] 132.168.73.247 |
instalguide [2016/07/25 10:49] (current) 132.168.72.225 |
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| This page describe the distribution content and how to run each of the 3 availables modes, after briefly presenting them. | This page describe the distribution content and how to run each of the 3 availables modes, after briefly presenting them. | ||
| + | |||
| + | ===== Requirements ===== | ||
| + | |||
| + | * 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 | ||
| + | * Optinal : Postgresql Server to be able to export data for further use with hEIDI. (See [[msidb|MSIDb]] page) | ||
| + | |||
| ===== What's in the distribution ? ===== | ===== What's in the distribution ? ===== | ||
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| 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 : | 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 : | ||
| <code> | <code> | ||
| - | > auto : directiry containing script samples for the automatique or batch mode. | + | > auto : directory containing script samples for the automatic or batch mode. |
| - | > db : Identification database creation script. Migration scripts for //old// identification databases will also be stored here. They will allow user to use existing databases with the new DB model needed for new IRMa version. | + | > 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 | > lib : libs and dll needed by IRMa | ||
| - | > VBscripts: Visual Basic scripts used to launch IRMa from Mascot Daemon. IRMa will be executed in automatique mode. | + | > VBscripts: Visual Basic scripts used to launch IRMa from Mascot Daemon. IRMa will be executed in automatic mode. |
| - | > IRMa-<version>.jar : IRMa librairy specific code | + | > IRMa-<version>.jar : IRMa library specific code |
| > *.bat : batch to run IRMa in specific mode. See following sections. | > *.bat : batch to run IRMa in specific mode. See following sections. | ||
| </code> | </code> | ||
| Line 24: | Line 37: | ||
| __Note__ \\ | __Note__ \\ | ||
| - | To validate //big// Mascot idenitification, it is possible to increase memory used by the application: | + | 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 carreful to not | + | 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 ! |
| - | Il est possible de modifier la mémoire occupée par IRMa. Pour cela il faut éditer le fichier run.bat et modifier le paramètre -Xmx<valeur>m. La valeur correspondant à la taille mémoire maximale allouée à IRMa en Mo. Attention cette valeur ne doit pas être équivalente (ou supérieur) à la taille disponible sur l'ordinateur. | + | |
| ==== Batch mode ==== | ==== Batch mode ==== | ||
| - | Pour cela exécuter le fichier //runBatch.bat//. \\ | + | Run batch file //runBatch.bat//. \\ |
| - | Le mode batch permet d'enchainer un ensemble d'opérations de façon automatique, et cela sur un ensemble d'identification Mascot ou de projets IRMa préalablement sauvegardés. | + | 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. | ||
| - | La description complète de la configuration d'[[batchUserGuide|IRMa Batch]] | + | A complete description of the use and configuration of [[batchUserGuide|IRMa Batch]] is available. |
| ==== Automatic mode ===== | ==== Automatic mode ===== | ||
| - | **Attention** le fichier //runBatch.bat// est un exemple d'utilisation. | + | **Attention** //runBatch.bat// file is only a example of how to run IRMa in this mode. |
| - | Le mode auto permet d'enchainer un ensemble d'opérations, décrit dans un fichier de script équivalent à celui utilisé pour le mode [[batchUserGuide|batch]], sur une identification donnée. Ce mode n'a donc aucune interface utilisateur. | + | 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 [[batchUserGuide|IRMa Batch]] documentation. This mode has no user interface. |
instalguide.1232436931.txt.gz · Last modified: 2009/01/20 08:35 by 132.168.73.247
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