Introduction

This page will explain how to obtain and start the PRIDE Converter 2 Tool Suite

Details

Download

Please download the latest release of the PRIDE Converter toolsuite from the Downloads section.

Unpack

The downloaded file will be a gzipped tarball that can be extracted using various tools (Winzip, Winrar, Stuffit Expander, tar, etc). When the archive is extracted, 2 files and one directory will be created:

lib/
pride-converter-2.0-SNAPSHOT.jar
converter.properties

Start

The PRIDE Converter 2 tools can work in both a command-line mode or in a full graphical user interface mode.

To start in command-line mode and display the CLI usage, you will need to open a shell/console/terminal and type the following command:

rcote@bobble:~/pride-converter$ java -jar pride-converter-2.0-SNAPSHOT.jar -help

This will result in the following information being displayed:

Usage: java -jar pride_converter.jar [mode]

PRIDE Converter 2
PRIDE Converter can operate in several different modes.
To launch the graphical mode simply specify no parameters.

The following modes are supported by PRIDE Converter:
   -converter    Launches the PRIDE Converter in convert mode.
                 This mode allows one to convert several search
                 engine result files into the PRIDE XML format.
   -filter       Launches the PRIDE Converter in filter mode.
                 This mode allows one to remove f.e. unidentified
                 spectra or a given set of proteins from an existing
                 PRIDE XML file.
   -merger       Launches PRIDE Converter in merger mode.
                 This mode allows one to merge several PRIDE XML files
                 into a single file.

For mode specific help please use java -jar pride_converter.jar [mode] -help

Please note that this assumes that the java executable is installed and in your application path. If this is not the case, please refer to the JAVA Help documentation on how to install Java on your computer.

To start in graphical, you will need to open a shell/console/terminal and type the following command:

rcote@bobble:~/pride-converter$ java -jar pride-converter-2.0-SNAPSHOT.jar

or simply double-click on the pride-converter-2.0-SNAPSHOT.jar file (assuming that jar files are associated with the java executable in your OS).