Extension:GbrowseImage
 | This extension is currently not actively maintained! Although it may still work, any bug reports or feature requests will more than likely be ignored. |
 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: Note: |
| Example | lacZ on EcoliWiki |
|
gbrowseImage |
|
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]- http://gmod.org/wiki/Gbrowse - The Generic Genome Browser
- http://gmod.org/wiki/GBrowse_img - The image-generator script for Gbrowse