Dazzle

From BioJava
Jump to: navigation, search

Contents

Dazzle

Dazzle is an easy to use server for the Distributed Annotation System (DAS).

It is implemented as a Java servlet, using the BioJava APIs. Dazzle is a modular system which uses small "datasource plugins" to provide access to a range of databases. Several general-purpose plugins are included in the package, and it it straightforward to develop new plugins to connect to your own databases.

Dazzle has been developed at the Wellcome Trust Sanger Institute by Thomas Down.

Getting Dazzle

Dazzle can be downloaded from http://www.derkholm.net/svn/repos/dazzle/trunk using subversion and built using ant:

svn checkout http://www.derkholm.net/svn/repos/dazzle/trunk ./dazzle
cd ./dazzle
ant clean
ant

copy the all the .jar files from the dazzle/lib/ dir into dazzle/dazzle-webapp/WEB-INF/lib directory. Then copy the dazzle/ant-build/dazzle.jar into the same dazzle/dazzle-webapp/WEB-INF/lib directory.

Edit the dazzlecfg.xml to put a "/" in front of filenames in the filename attributes values e.g. <string name="fileName" value="test.embl" /> should be changed to <string name="fileName" value="/test.embl" />, there are 3 instances of this in the default dazzlecfg.xml file.

Note that the above download includes biojava, and some other JARs that you may find useful (and impossible to track down elsewhere). By default it is using the jar files located in the jars subdirectory. If you have your own installation of biojava please copy it there or update the build.xml to point to your path. Note that on your system you may need to use "ant -lib jars" instead of "ant" above.

Installation and Configuration

For installation and configuration instructions, please see the Dazzle:deployment guide.

For learning how to write your own Dazzle plugins, please see the Dazzle:writeplugin tutorial.

For learning how to deploy an Ensembl DAS reference server see the instructions here.

If you want to follow Dazzle development, you can obtain up-to-date source code via Subversion from http://www.derkholm.net/svn/repos/dazzle/.

Available Plugins

There are a number of ready made plugins available that can be set up with simply configuring dazzlecfg.xml correctly. For instructions how to write your own plugin go to Dazzle:writeplugin

DAS Extensions

Dazzle provides support for the DAS extensions that are available in the DAS 1.53E specification

DAS client

The BioJava based DAS client library Dasobert is available from http://www.spice-3d.org/dasobert/

Personal tools
Namespaces
Variants
Actions
Documentation
Community
Toolbox