Extension:GbrowseImage

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MediaWiki extensions manual
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gbrowseImage
Release status: beta
px
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 From GitHub
Example lacZ on EcoliWiki
gbrowseImage
Translate the GbrowseImage extension if it is available at translatewiki.net
Check usage and version matrix.

What can this extension do?[edit]

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[edit]

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[edit]

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[edit]

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

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

Configuration parameters[edit]

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[edit]