====== Set up Proline Suite with Proline-Admin GUI ======

__Note__ : All the settings shown on the screenshots only stand for examples. You must adapt them to your needs.

You must first configure ProlineAdmin since this component is used to create the databases needed by Proline.

===== Launch Proline-Admin GUI =====

If you used the Windows installer, a shortcut "Proline Admin" is available in the Windows Start Menu, under the Proline folder.

Otherwise, execute the ''start.sh'' or  ''start.bat'' script located in the Proline Admin GUI folder.

===== Configure Proline Suite=====

==== Locate configuration files ====

At application start, the default configuration file ''config/application.conf'' is loaded. Note that, when using Proline Admin (GUI) for the first time, this file isn't valid and will lead to an error message. Don't bother: you can alternatively edit this file  or select another ''.conf'' file of the same format using the //Configuration// window: \\
- On the main page, click on //Configuration// to open that window (screenshot below). \\
- The first tab, named //Configuration files//, let you choose all the configuration files that you may use in this application. 
  * The first one is the __Proline-Admin configuration file__. This is the only one required for a basic use of the application (setup and upgrade Proline, create users and projects).
  * The second one is the __Proline server configuration file__. It is optional for the actions described above, but mandatory to edit the Proline Server configuration (see the section Configuring the mount points).
  * The third one is the __Proline PWX (Proline Web eXtension) configuration file__. It is optional too, and useful only if you use the web interface of Proline (Proline Web). Mentioning it will allow you to automatically synchronize the mount points between the Proline server and the web interface.
  * The last field is the __PostgreSQL data directory__, mandatory to configure PostgreSQL //via// ProlineAdmin GUI ([[setupguide:postgresqloptimization|see PostgreSQL optimization and authorizations]]).
- Click //OK// to save changes and go back on the main page, or //Apply// to save changes and stay on the configuration window (edit files).\\

**NB:** The Proline server folder is located in the ".\ws" sub-folder of the Proline installation directory if Windows installer has been used. If archive files has been used you will find it under the folder where you have unzipped the "Proline Server" archive. The Proline server folder should contain a sub-folder named ''ProlineWeb-Core-<x.y.z>''. \\
The configuration file is located at ''<proline_server_folder>\ProlineWeb-Core-<x.y.z>\Proline\WEB-INF\classes''.\\

{{ :setupguide:choose_config_custom.png?nolink&1200 |}}


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==== Configure Proline parameters ====

To edit Proline configuration file(s), select the last tab of the configuration window, entitled //Proline configuration//.

{{ :setupguide:proline_configuration.png?nolink&800 |}}

This tab is split in three parts:
  * __Working files__ (not visible on the screenshot above): reminds you of the selected configuration files. You can also select other files from here ; it will be effective after clicking on the //Apply// button of this block. It is fully synchronized with the first tab (//Configuration files//) of the configuration window.
  * __Database connection:__ configure and test the connection to the proline database. Entries will be saved in Proline Admin configuration file and in Proline Server configuration file if provided.
  * __Mount points:__ define the Proline mount points in three categories (more details in the following paragraph). Entries will be saved in Proline Server and PWX configuration files if provided.

=== Configure the mount-points ===

Note that the section named //Mount points// is enable only if the Proline server configuration file has been located (see screenshot above).

Input files (e.g. *.RAW, *.WIFF, *.D) should be set in the 'Raw files' sub-section.\\
mzDB files should be set in the 'mzDB_files' sub-section.\\
Identification result files (e.g. Mascot .dat, OMSSA .omx) should be set in the 'Result files' sub-section.

Several alias/full_path pairs can be used or each.
Aliases can be any valid string chosen by the administrator to help the users identify a mount_point. If multiple repositories are defined, aliases must be different.

!! Important: on a Windows server installation, please use UNC style to access remote disks instead of mounted disk on letters. Otherwise Proline won't be fully functional.
ex: use \\\\my_server\\disk\\folder 
instead of a mounted disk on Z: (Z: mounted as \\my_server\\disk\\folder)

Result identification files (Mascot dat,  OMSSA or X!Tandem) as well as mzDB files (for the XIC Quantitation process) are only browsed from Proline Server side. 

Click //OK// to save changes and go back on the main page, or //Apply// to save changes and stay on the configuration window (edit files).\\

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==== Set up the Datastore ====

Once the configuration files has been edited and validated, the button //Set up Proline datastore// becomes availale in the main page. Click it to finish the Datastore setup.

__Note__: This functionality will be disabled if Proline is already set up or if Proline configuration is invalid.

{{ :setupguide:setup_proline_datastore.png?nolink&1000 |}}
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