The JBrowse TWiki plugin
We have created a minimal TWiki plugin for JBrowse, located in the twiki/
directory of the JBrowse source tree.
- Install TWiki in
- Install JBrowse in
- Create symlinks to JBrowse from TWiki:
cd /usr/local/jbrowse/twiki; make
Internally, the plugin regularly runs a Makefile
to automatically maintain prepared JBrowse server files for uploaded FASTA, GFF, BED & WIG-format attachments to wiki pages.
If the string
appears anywhere in the wiki "plaintext" for the page (e.g. in an automatically-included header), the rendered page will contain an embedded JBrowse browser,
serving up the page's attachments as tracks.
JBrowse configuration files can also be attached, with the filename
, to split .gff file attachments into multiple tracks using various glyphs & styles.
This plugin stops some way short of being everything that one would hope for in a GenomeWiki
It lacks fine-grained access controls, an intuitive JBrowse-integrated UI, robust Wikipedia:ACID
properties, a Wikipedia:distributed_database
, and other features.
Primarily it's meant to illustrate a simple declarative-dependency approach to creating a JBrowse Wikipedia:plugin
for a web Wikipedia:content_management_system
However, it could
feasibly be used as a view onto a genome consortium wiki, such as this 12-fly wiki
(NB: that wiki uses the Wikipedia:MediaWiki
engine, but the Makefile approach used here would be easy to port to MediaWiki.)
The plugin is up & running here on a TWiki 4.0 installation:
We have not yet integrated it into the main biowiki.org TWiki, since it's experimental software.
(Also, the main wiki engine @biowiki.org is a modified TWiki 2004 release as of 20 Mar 2009).
- 20 Mar 2009
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