Installation
Plugins can be downloaded and installed directly through the browser by choosing Plugins > Plugin Manager > Install from Repository.
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Plugins
Compatible with 1.5.0
Analytics
SNP Finder Plugin
Description: Detects SNPs from read alignments based on the percentage mismatches.
Authors: Michael Brudno, Marc Fiume
Contact: mfiume [at] cs [dot] toronto [dot] edu
RNA-Seq Analyzer
Description: Plugin allows visualisation and analysis of GTF data for isoform identification and abundance estimation.
Manual: click here
Author: Aziz Mezlini
Database
1000 Genomes Alignment Browser
Description: Load alignments from the 1000 Genomes Project FTP server.
Author: Eric Smith
SQL Plugin
Description: Provides access to SQL databases.
Author: Eric Smith
UCSC Plugin
Description: Provides access to the UCSC genome database.
Author: Eric Smith
Information & Statistics
Table View
Description: Displays information about the records in frame in a tabular format.
Authors: Marc Fiume, Andrew Brook, Vanessa Williams
Note: This plugin comes pre-installed when you download Savant.
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Development
The Savant Software Development Kit (SDK) is a set of tools that allows for development and testing of extensions to the browser, including plugins. A sample plugin is included in the SDK distribution.
Download the current Savant SDK (updated for Savant 1.5.1).
To learn how to develop a Savant Plugin, follow the Plugin Development Tutorial.
Beta SDK
Savant SDK 2.0 Alpha is now available. A full version is expected to be released January 2012, before the release of Savant 2.0.
Changes since 1.6.0:
- A large number of classes which were formerly internal to Savant have now been moved to the savant.api packages. For instance, the various Event classes have been moved to the savant.api.event package, while abstract classes representing the Savant record data-types have been created in savant.api.data. The intent is that it should now be possible to implement all the functionality of any plugin without referring to any Savant classes outside the savant.api.* tree
- The format of the plugin.xml file has been simplified. Examine the plugin.xml files included with the SDK to see what your plugin.xml file should now look like.
- In addition to the existing SavantPanelPlugin and SavantDataSource plugin classes, there is a third plugin type, ToolPlugin, which can be used to wrap command-line tools such as GATK. Documentation for ToolPlugins will be forthcoming.