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Extension:GbrowseImage

MediaWiki extensions manual
OOjs UI icon advanced.svg
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.

UsageEdit

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 instructionsEdit

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.

InstallationEdit

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

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

Configuration parametersEdit

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 alsoEdit