ProViewer

ProViewer is an interactive web visualisation plug-in for the mzIdentML file within the Galaxy bioinformatics platform. In the repository, we provide the necessary files to install ProViewer plugin into your existing Galaxy instance accomplished with the source codes of the underneath functionality which converts mzIdentML into JSON files to be viewed in the main panel. Main folders of the repository are as follows:

• ProViewer - Galaxy visualisation plugin
  • Proviewer - client-side of the plugin
  • webcontroller - server-side of the plugin
  • tool/mzIdentMLToJSON - Galaxy tool
  • samples - sample configurations and other sample files
• ProExtractor - source code of thr Java library developed for mzIdentML data extraction
• GIOServer - GIO server specific installation files
• install.py - installation setup
• Test
• Documentation

Galaxy visualisation plugin cient-side and server-side files are organised into two folders which are called proviewer and webcontroller respectively. Additionally, we have a Galaxy tool called "mzIdentMLToJSON" which generates temporary JSON files to speed up data loading for visualisation plugin. You must integrate both plugin and tool in order to work with the visualisation, as Galaxy tool contains dependency files for the visualisation plugin too. Although the integration of both plugin and tool is mandatory for installation, you can use plugin independently without using Galaxy tool. However, we strongly recommend to use our Galaxy tool prior to visualise mzIdentML files for a much faster visualising speed.

This plugin is already installed on our own Galaxy server, GIO. Scroll down to the How to use ProViewer plugin section below to find out how to use it. Or click here to see a two minute demo. There is also a ProViewer poster.

Installation

Installation instructions are provided below. These instructions assume that you already have Galaxy installed and have admin access to that installation. If you do not already installed Galaxy or not having admin access, please refer link here.

In order to proceed, please download our repository to your machine by cloning the repository. If you download as a zip file, then extract the zip folder.

Install Galaxy Visualisation Plugin

Step 1 - Edit the configuration file

You need to make sure, you have enabled visualisation plugins on your Galaxy installation. First, go to your galaxy.ini configuration file (located in <your galaxy directory>/config/). If you do not have a galaxy.ini file, but have a galaxy.ini.sample file, then makes a copy of galaxy.ini.sample file and rename it to galaxy.ini. Secondly, search for visualization_plugins_directory setting in that galaxy.ini file. If this setting has not already set, assign your visualisation directory/uncomment the (last) line as follows:

# Visualizations config directory: where to look for individual visualization plugins.
# The path is relative to the Galaxy root dir. To use an absolute path begin the path
# with '/'.
visualization_plugins_directory = config/plugins/visualizations

Step 2 - Run the installation setup file

Go to the downloaded folder of the repository from the command-line, and execute the install.py file as python install.py and follow the given instructions. "Quick install" option will use all the default settings, where "advanced install" option allows to customise settings at the time of the installation. Examples are provided for both quick and advanced installation as a guide. Please follow same format when you provide file paths, especially / at the end where required. This setup will perform following actions:

• copy installation files to your server
• add all the plugin settings into a settings file called proviewer_settings.ini into <your galaxy directory>/config/ location
• A backup file will be created for datasets.py file with the file name including a current timestamp in <your galaxy directory>/lib/webapps/galaxy/api location.

Install Galaxy Tool

Step 1 - Configure Tool

Locate the tool_conf.xml configuration file in <your galaxy directory>/config/ location. If you do not find a tool_conf.xml file, but have a tool_conf.xml.sample file, make a copy of it and rename new file as tool_conf.xml. There, add these parameters anywhere of the file under <toolbox> tag:

<section id="PSI" name="PSI Standards" >
    <tool file="mzIdentMLToJSON/mzIdentMLToJSON.xml" />
</section>

As a guidance for above step, sample configuration file is given in samples folder.

That's it! You are ready to use the visualisation plug-in and the tool.

Note: You must restart the server to reflect the changes.

How to use ProViewer plugin

User MUST login to the server in order to use visualisation functionality. This visualisation is enabled for mzIdentML files only. Once you upload mzIdentML file(.mzid file extension), it will be added to the history panel. You can visualise the input mzIdentML file by clicking on the visualisation button and selecting the ProViewer from the menu. Time taken to load data into the viewer depends on the size of the input file.

How to use ProViewer tool

You can integrate this tool into your protein identification workflows or can execute individually. If you are using search tool in the workflow, the output mzIdentML file of the search tool is the input for this galaxy tool.

Dependencies

• Python 2.7
• JRE 8