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--- setupguide:firstinstall [2015/07/08 09:32]
130.79.67.200 [Locating the server folder]
+++ setupguide:firstinstall [2016/07/07 10:07] (current)
132.168.72.225
@@ Line 1: / Line 1: @@
-====== Installing the Proline Suite ======
+====== OBSOLETE Installing the Proline Suite ======
+**This page is an obsolete help file. Please see following description :  ** [[setupguide:start#installing_upgrading_the_proline_suite|Install and set up Proline]]
 The Proline suite is based on ([[setupguide:start#architecture_overview|different components]]).
 The following documentation describes the installation procedure for each of this component:
-  * [[#proline_server_installation_and_setup|Proline server]]
+  * [[#installing_and_configuring_proline_server|Proline server]]
   * [[#installing_and_configuring_the_sequence_repository|Sequence Repository]]
   * [[#installing_proline_studio|Proline Studio]]
   * [[#installing_and_configuring_proline_web_desktop|Proline Web]]
-====== Proline server installation and setup ======
+====== Installing and configuring Proline server ======
-==== Proline server installation ====
+===== Proline server installation =====
 === Windows users ===
-Download the automated installer from the Proline website (http://proline.profiproteomics.fr/download/).
+Download the automated installer from the Proline website (http://proline.profiproteomics.fr/download/). \\
+**Warning: Be sure to run the executable file as "administrator" to be able to install third-party dependencies such as PostgreSQL**.
 The wizard will guide you through the installation process. \\
 By default, the installer will unpack all components on the computer. However, it is possible to install the Proline components on distinct computers if it fits better your hardware architecture.
-For users who prefer **manual installation or witout administrator rights**, an archive file of the distribution is also available. You can follow the installation procedure described in the next section.
+For users who prefer **manual installation or without administrator privileges**, an archive file of the distribution is also available. You can follow the installation procedure described in the next section.
@@ Line 33: / Line 39: @@
   * Sequence Repository
-Unzip these components on the appropriated computer (Proline Server and Proline Admin is recommanded to be on the same computer. Sequence Repository is recommanded to be installed on the computer where fasta files are accessible)
+Unzip these components on the appropriated computer (Proline Server and Proline Admin is recommended to be on the same computer. Sequence Repository is recommended to be installed on the computer where fasta files are accessible)
 Once Proline is installed you must initialize Proline datastores and settings.
@@ Line 41: / Line 47: @@
 We will guide you through this process, step by step, using both these tools.
-===== Setting up the Datastore =====
+===== Setting up the Datastore and Proline Server =====
-You must first configure ProlineAdmin since this component is used to create the databases needed by Proline.
+You can either use the graphical interface ProlineAdmin GUI => [[setupguide:setup_with_prolineadmin_gui#setup with prolineadmin gui| How to ]] \\
+or use the command-line tool ProlineAdmin  => [[setupguide:setup_with_prolineadmin#setup_with_prolineadmin| How to ]] .
-==== From graphical tool ProlineAdmin GUI ====
-=== Launch ProlineAdmin GUI ===
-== Windows users ==
-A shortcut "Proline Admin" is available in the Windows Start Menu, under the Proline folder.
-== Linux users or manual installation  ==
-Execute the ''start.sh'' script located in the folder obtained after Proline Admin GUI archive file extraction.
-=== ProlineAdmin GUI usage ===
-The default configuration file ''config/application.conf'' is loaded. You can alternatively edit this file (see [[#configuring_prolineadmin|"Configuring ProlineAdmin"]] section below) or select another ''.conf'' file of the same format.
-To edit default file, press the "Edit Proline configuration" button. You can now edit your file in the newly opened window, and save it.
-{{ :setupguide:edit_config_bg.png?nolink&600 |}}
-To load a ''.conf'' file, use the menu on the top left and select your file in the file browser.
-{{ :setupguide:select_config_file.png?nolink&600 |}}
-Finish the datastore setup by clicking the newly available button "Set up Proline".
-__Note__: This functionnality will be disabled if Proline is already set up or if Proline configuration is invalid.
-{{ :setupguide:set_up_proline.png?nolink&600 |}}
-==== Using the command line interface (ProlineAdmin) ====
-Edit the configuration file ''config/application.conf'' located in the ProlineAdmin folder (see [[#configuring_prolineadmin|"Configuring ProlineAdmin"]] section below).
-Then perform the datastore setup by running the dedicated script.
-== Windows users ==
-The ProlineAdmin program files are located in the ".\admin" sub-folder of the Proline installation directory.
-You should find the following script in this folder:
-<code>
-> setup_proline.bat
-</code>
-== Linux users or manual installation  ==
-Execute the ''setup_proline.sh'' script located in the folder obtained after Proline Admin GUI archive file extraction.
-==== Configuring ProlineAdmin ====
-Modify the following lines to fit your DBMS configuration :
-<code>
-proline-config {
-  driver-type = "postgresql" // valid values are: h2, postgresql or sqlite
-  data-directory = "/Path/to/Proline/Data"  //Not used actually...
-}
-auth-config {
-  user="proline_user"  // !! SET TO Database Proline user login
-  password="proline_user_password" // !! SET TO Database Proline user password
-}
-host-config {
-  host="your_postgresql_server_host"  //!! Do NOT put "localhost", but the real IP address or fully qualified name
-  port="5432" //or other port used to access your DBMS
-}
-</code>
-__Note__: default naming scheme of databases created by Proline can be modified by editing ''config/application-<dbtype>.conf'' file.
-===== Configuring the Proline Server =====
-==== Locating the server folder ====
-=== Windows users ===
-The server program files are located in the ".\ws" sub-folder of the Proline installation directory.
-=== Linux users or manual installation ===
-Open 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>''.
-=== Editing the configuration file===
-The configuration file is located at ''<proline_server_folder>\ProlineWeb-Core-<x.y.z>\Proline\WEB-INF\classes''. \\
-== Configuring the datastore ==
-Edit the ''application.conf'' file in the same way you did it for ProlineAdmin (see [[#Setting up the Datastore]]).
-If your configuration is valid, the Proline Server will be able to use the datastore you've created using Proline Admin.
-== Configuring the mount-points ==
-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.
-Administrator must configure the target directory/ies in the entry ''mount_points'' in the ''application.conf'' file
-Mascot dat or OMSSA path should be configured in ''result_files'' sub-entry, administrator can add one or more mappings as ''label = "<absolute/directory/path>"''.
-mzDB files path should be set under ''mzdb_files'' sub-entry.
-Label can be any valid string chosen by Administrator to help user identify mount_point. If multiple repositories are defined, labels must be different.
-Configuration examples :
-<code>
-mount_points {
-  result_files {
-    mascot_data = "Z:/"  //under window environement
-    omssa_data = "/local/omssa/data" //under linux environement
-    xtandem_data = "U:/"
-    ...
-  }
-  ...
-  mzdb_files {
-  }
-}
-</code>
 ===== Running the server =====
 Administrator can change default amount of memory used by the server in the ''jetty-runner.bat'' /''jetty-runner.sh'' file. If the server is configured with large amount of memory, it is recommanded to increase this value.
-Change the value of -Xmx option : Xmx4g => -Xmx9g to pass from default 4 GO to 8GO.
+Change the value of -Xmx option: Xmx4g => -Xmx9g to pass from default 4 GO to 8GO.
-Run ''jetty-runner.bat'' (or jetty-runner.sh on linux system) to start the jetty server. You should now be able to access ProlineWeb-Core by typing   [[http://localhost:8080/proline]] or[[http://<host>:8080/proline]] in your favorite browser. The following message must appear :
+Run ''jetty-runner.bat'' (or jetty-runner.sh on linux system) to start the jetty server. You should now be able to access ProlineWeb-Core by typing   [[http://localhost:8080/proline]] or [[http://<host>:8080/proline]] in your favorite browser. The following message must appear:
 <code>
@@ Line 190: / Line 77: @@
 ====== Installing and configuring the Sequence Repository ======
-Even if this is an optionnal module it is recommended to install it, mostly if you want to view the proteins sequences in the user interfaces !
+Even if this is an optional module it is recommended to install it, mostly if you want to view the proteins sequences in the user interfaces!
 It can be installed on the same machine running the Proline Server. However as this module will parse the mascot fasta files to extract sequence and description from it, it will be more efficient if installed on the computer executing your Mascot Server. In any case, you should also be able to access to the PostgreSQL server from the computer where Sequence Repository is installed.
@@ Line 219: / Line 106: @@
 </code>
-__note__ :
+__note__:
   * If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so <code>javax.persistence.jdbc.url=jdbc:postgresql://<host>:5432/uds_db</code>
@@ Line 227: / Line 114: @@
 As this module is used to extract Protein Sequence, description from a fasta file for a specific protein accession, it is necessary to configure the rule used to parse the protein ACC, from fasta description line. This is similar to the rules specified in Mascot Server.
-To do this, //retrieve-service.properties// file should be edited. In this file it is necessary to escape (this means prefix with '\') some characters : '\' , ':' and '='
+To do this, //retrieve-service.properties// file should be edited. In this file it is necessary to escape (this means prefix with '\') some characters: '\' , ':' and '='
 <code>
@@ Line 253: / Line 140: @@
   * fr.proline.module.seq.localFASTAPaths : only one instance should be defined. For linux system, fr.proline.module.seq.localFASTAPaths=/local/data/fasta;/local/mascot/sequence
   * fr.proline.module.seq.defaultReleaseRegex : Regular expression to extract release version (CASE_INSENSITIVE) from the fasta files.
-  * fr.proline.module.seq.uniProtSEDbNames : Regular expression to identify Uniprot like fasta. The entry of theses files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession.
+  * fr.proline.module.seq.uniProtSEDbNames : Regular expression to identify Uniprot like fasta. The entry of these files will be parse using specific rule (fr.proline.module.seq.uniProtSEDbIdentifierRegex) to extract protein accession.
 For other fasta files the protein accession will be extracted by using the string before the first blank space.
@@ Line 266: / Line 153: @@
     * [[prolineconcepts:PWD| Install, Configure and launch the Desktop]]

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