Extension:GbrowseImage

What can this extension do?
Displays an image of a genomic region using the  tag in the wikitext of a page. Clicking the image takes the user to the underlying GBrowse instance.

Usage
Essentially, this extension is a PHP wrapper for the gbrowse_img script that comes packaged with GBrowse.

This extension takes a set of parameters wrapped in a set of  html-style tags and create a clickable picture. Most (if not all) of the parameters are named after the equivalent gbrowse_img settings for consistency. The parameters are simple key=value pairs within the  tags.

Example:  name=NC_010473:430647..432578 source=ecoli_DH10B preset=GeneLocation 

Download instructions
Please cut and paste the code found below and place it in. Note: $IP stands for the root directory of your MediaWiki installation, the same directory that holds LocalSettings.php.

Installation
To install this extension, add the following to LocalSettings.php:

This extension requires that the Mediawiki setting $wgAllowExternalImages be turned on. In LocalSettings.php you can add:

Configuration parameters
Currently none, but it would make sense for the hard-coded settings in the script to be configured via LocalSettings.php.

Note about the script: there are some constants set (around lines 54-63) that will need changing. At EcoliWiki we show 1000bp on either side of the gene. This is set by the PADDING_LENGTH constant. It can be set to 0. There are two other constants that need changing, the URLs to gbrowse and gbrowse_img, respectively.