The Proline suite is based on (different components). The following documentation describes the installation procedure for each of this component:

• Proline server
• Sequence Repository
• Proline Studio
• Proline Web

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 without administrator privileges, an archive file of the distribution is also available. You can follow the installation procedure described in the next section.

There is no automated installer at the moment.

First check that all requirements are first installed on the computer.
Then download the zip archive containing Proline components from the dedicated website(http://proline.profiproteomics.fr/download/).

The Proline Server archive file contains three others archives corresponding to the (different components).

• Proline WebCore : the Proline Server
• Proline Admin GUI
• Sequence Repository

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.

On this purpose, the Proline-Admin software is provided with the Proline Suite. It is available as a command-line tool or as Graphical Interface called Proline-Admin GUI.

We will guide you through this process, step by step, using both these tools.

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

A shortcut “Proline Admin” is available in the Windows Start Menu, under the Proline folder.

Execute the start.sh script located in the folder obtained after Proline Admin GUI archive file extraction.

The default configuration file config/application.conf is loaded. You can alternatively edit this file (see "Configuring ProlineAdmin" section below) or select another .conf file of the same format. To select a file, go to the “Select configuration files” menu. A dialog opens, offering you to chose 2 files:

• the first one is the ProlineAdmin configuration file, mandatory to use configure, setup and upgrade Proline, as well as create users and projects;
• the second one is the Proline server configuration file. This one is optional for the actions described above, but mandatory to edit Proline mount points (see section 'Configuring the mount-points'). Additionally, if this file is selected, it will be automatically synchronized with ProlineAdmin's configuration file.

To edit Proline configuration file(s), press the “Edit Proline configuration” button. You can now edit your file(s) in the newly opened window, and save it.

Finish the datastore setup by clicking the newly available button “Set up Proline”.

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

Edit the configuration file config/application.conf located in the ProlineAdmin folder (see "Configuring ProlineAdmin" section below). Then perform the datastore setup by running the dedicated script.

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:

> setup_proline.bat

Execute the setup_proline.sh script located in the folder obtained after Proline Admin GUI archive file extraction.

Modify the following lines to fit your DBMS configuration:

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
}

Note: default naming scheme of databases created by Proline can be modified by editing config/application-<dbtype>.conf file.

The 'data-directory' key under 'proline-config' indicates where to store Proline data (e.g. exports). It must not be confused with 'postgresql-data-dir', which references the PostgreSQL data directory (data and configuration files for PostgreSQL). The “postgresql-data-dir” is needed to configure your PostgreSQL instance through ProlineAdmin-GUI (see PostgreSQL optimization).

postgresql-data-dir = "<path/to/postgresql/data-dir>"

Using ProlineAdmin-GUI will also require to specify the full path to Proline Server (aka WebCore) configuration file (initially named application.conf):

server-config-file = "<path/to/webcore/application.conf>"

Note: Both 'postgresql-data-dir' and 'server-config-file' fields can be configured in the ProlineAdmin-GUI menu.

The server program files are located in the “.\ws” sub-folder of the Proline installation directory.

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>.

The configuration file is located at <proline_server_folder>\ProlineWeb-Core-<x.y.z>\Proline\WEB-INF\classes.

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.

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

!! 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)

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:

mount_points {

  result_files {
    mascot_data = "Z:/"  //under window environement
    omssa_data = "/local/omssa/data" //under linux environement
    xtandem_data = "U:/"
    ...
  }
  ...
  
  mzdb_files {
  }

}

Mount points can be edited using ProlineAdmin GUI. As it is explained in the 'Setting up the Datastore' section, first make sure Proline server configuration file is selected. Then click on the 'Edit Proline configuration button' to access configuration panel.

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.

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:

ProlineWeb-Core working !

Number of IVersion services : <X>
fr.proline.core.wsl.Version Module: ProlineWeb-Core Version: <XXX>
fr.proline.module.parser.omssa.Version Module: PM-OmssaParser Version: <YYY>
fr.proline.module.parser.mascot.Version Module: PM-MascotParser Version:<XYZ>
fr.proline.admin.Version Module: Proline-Admin Version: <ZYW>
fr.proline.util.ScalaVersion Module: ProFI-Commons-Scala Version: <YZX>
fr.proline.util.JavaVersion Module: ProFI-Commons-Java Version: <YXZ>
fr.proline.core.service.Version Module: Proline-OMP Version: <WYZ>

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.

Select this component from the wizard of the automated installer. The corresponding program files will be located in the “.\seqrepo” sub-folder of the Proline installation directory.

This module is distributed as an archive file (embedded in Proline Server archive) and need to be extracted in your preferred folder to be installed.

Configuration files are located under the “<seqrepo_folder>/config”.

Datastore description

pg_uds.properties file define datastore description to access to the UDS database (for postgresql database):

javax.persistence.jdbc.driver=org.postgresql.Driver
javax.persistence.jdbc.url=jdbc:postgresql://<host>:<port>/<uds_db>
javax.persistence.jdbc.user=<user_proline>
javax.persistence.jdbc.password=<proline_user_password>

note:

• If you didn't change the default naming scheme of databases the <uds_db>= 'uds_db' so

  javax.persistence.jdbc.url=jdbc:postgresql://<host>:5432/uds_db

• proline_user_password and user_proline are the same as specified in application.conf for Proline Admin or Proline WebCore

Protein description parsing rule

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 '='

# Name of the UDS Db configuration file (Java properties format)
fr.proline.module.seq.udsDbConfigurationFile=pg_uds.properties

# Paths must exist (regular file or directory) and multiple paths must be separated by ';' character
fr.proline.module.seq.localFASTAPaths=Y\:\\sequence;D\:\\Temp\\Admin\\FASTAs

# Java Regex with capturing group for SEDbInstance release version string (CASE_INSENSITIVE)
fr.proline.module.seq.defaultReleaseRegex=_(?:D|(?:Decoy))_(.*)\\.fasta

# UniProt style SEDb (FASTA file name must contain this Java Regex CASE_INSENSITIVE) multiple Regex separated by ';' character
fr.proline.module.seq.uniProtSEDbNames=\\AUP_;ISA_D

# Java Regex with capturing group for SEDbIdentifier value (without double quote)
# UniProt EntryName ">\\w{2}\\|[^\\|]*\\|(\\S+)"
# UniProt UniqueIdentifier (primary accession number) ">\\w{2}\\|([^\\|]+)\\|"
# GENERIC Regex ">(\\S+)"
fr.proline.module.seq.uniProtSEDbIdentifierRegex=>\\w{2}\\|[^\\|]*\\|(\\S+)

Note:

• 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 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.

• Proline Studio application distribution is a zip file that must be extracted on each client computer.

• Install, Configure and launch the Desktop