Integration

http://genomeview.org/content/integration

Other topics that may be of interest: <a href="/content/integrating-genomeview-editor">Integrating as editor</a> and <a href="/content/communicating-genomeview">Communicating with GenomeView</a>

This page tries to explain how to integrate GenomeView in your website with your data. You can either make it available through Java Webstart, or as an applet. Whenever possible we recommend using Java Web Start as it has better cross-platform and cross-browser support.

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Present your data through a Java Web Start link

The fastest and simplest way to get started and with integrating GenomeView with your data is by directly constructing a webstart link.

The default launch URL is located at http://genomeview.org/start/launch.jnlp. If you require a specific version, there are stable URLs available from the supported versions page.

The next step is constructing your URL to load sequence and features. Below a sample URL, which will load some sequence with annotation and some short reads. It will start with the [100000,200000] region visible.

http://genomeview.org/start/launch.jnlp?--position 100000:200000 --url http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.fasta http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.gff.gz http://www.broadinstitute.org/software/genomeview/demo/c_elegans/uwgs-rw_L2_FC6218_3.CHROMOSOME_IV.sorted.bam.bai

Pasting this URL in your browser will start GenomeView with data from C. elegans loaded.

Command line options to GenomeView can be added after the question mark after the installation URL.

The formalized version of the integration URL looks like this:

http://genomeview.org/start/launch.jnlp?[command line options for GenomeView separated with spaces]

Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.

Present your data through a Java Web Start session (recommended)

A session file is a text file that contains instructions for GenomeView on which data to load and how to configure itself.

The basic set-up to start GenomeView with a session file is

http://genomeview.org/start/launch.jnlp?--session <URL to the session file>

For example http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php

Embedding GenomeView as an applet

Support for the applet version of GenomeView is currently on hold due to ever changing Java support from the various browser and OS vendors. It is impossible to maintain any semblance of stability. All of the material below may or may not work.

The key code that needs to be included in the body of your web page is:

<script type="text/javascript" src="http://www.java.com/js/deployJava.js"></script>
<script type="text/javascript" src="http://genomeview.org/start/genomeview.js"></script>

<script type="text/javascript">
    	var gv_url		= null;
     	var gv_config	= 'http://genomeview.org/jsdemo/democonfig.txt';    
     	var gv_extra	= null;
       	var gv_location	= null;
        startGV(gv_url,gv_location,gv_config,gv_extra,500,400);
</script>

The gv_url can be used to pre-load a reference sequence. This file will be loaded first and only then will GenomeView proceed with loading additional data.

The configuration file you want to use, can be specified using the gv_config option.

All other data that you want to have loaded can be specified in a space separated list in gv_extra. These data sets will be loaded in parallel.

The location that will initially be visible, can be set by gv_location. The position is in the format <entry>:<start position>:<end position> The entry part is optional can be omitted in which case it becomes <start position>:<end position>

Note: we strongly recommend you use the genomeview.js we provide as that's the one we keep up to date with progressing releases.