Extension:GbrowseImage

Category:Unmaintained extensions#GbrowseImage Category:Extensions without a compatibility policyCategory:Extensions with unknown license
MediaWiki extensions manual
gbrowseImage
Release status: unmaintainedCategory:Unmaintained extensions
Implementation MediaCategory:Media handling extensions, Hook Category:Hook extensions
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+Category:Extensions with manual MediaWiki version
License GPL?
Download

GitHub:

Note:
No localisation updates are
provided by translatewiki.net .

Category:Extensions in GitHub version control
Example lacZ on EcoliWiki
Tags
gbrowseImage
Hooks used
Category:All extensionsCategory:Extensions not in ExtensionJson

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 that comes packaged with GBrowse .

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

Category:All extensions Category:Extensions in GitHub version control Category:Extensions not in ExtensionJson Category:Extensions with manual MediaWiki version Category:Extensions with unknown license Category:Extensions without a compatibility policy Category:Hook extensions Category:Media handling extensions Category:ParserFirstCallInit extensions Category:Unmaintained extensions