Extension:GbrowseImage

MediaWiki extensions manual

gbrowseImage Release status: unmaintained
Implementation	Media, Hook
Description	Creates an image from a given GBrowse in a wiki page.
Author(s)	Daniel Renfro, Jim Hu (DanielRenfrotalk)
Latest version	0.2 (2010-07-19)
MediaWiki	1.12+
License	GPL?
Download	GitHub: project page git repository URL [help ] commit history Note: No localisation updates are provided by translatewiki.net .
Example	lacZ on EcoliWiki
Tags gbrowseImage
Hooks used ParserFirstCallInit

What can this extension do?

Displays an image of a genomic region using the <gbrowseImage> 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 [1] that comes packaged with GBrowse [2].

This extension takes a set of parameters wrapped in a set of <gbrowseImage> 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 <gbrowseImage> tags.

Example:

<gbrowseImage>
name=NC_010473:430647..432578
source=ecoli_DH10B
preset=GeneLocation
</gbrowseImage>

Download instructions

Download a snapshot from GitHub following the download link in the infobox.

Unzip the code and place the newly created folder to your extensions directory.

Installation

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

require_once("$IP/extensions/GBrowseImage/gbrowse_img.php");

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.

See also

• http://gmod.org/wiki/Gbrowse - The Generic Genome Browser
• http://gmod.org/wiki/GBrowse_img - The image-generator script for Gbrowse