Make a copy of the ~/tools/data_source/biomart.xml for your local biomart
install, and change the action in the following tag to point to it.
<inputs action="http://www.biomart.org/biomart/martview" check_values="false"
Then add your new biomart tool wrapper to your tool_conf.xml file and start up
your Galaxy instance.
For details about adding a new tool, see
Greg Von Kuster
On Mar 26, 2011, at 10:19 AM, Andrea Edwards wrote:
> I have looked at the biomart plugin for Galaxy and this seems to allow access
> to marts on the biomart central server.
> Is there anyway to use this plugin to access a biomart on my server if I
> can't make my biomart available on the biomart central server.
> If not, would it be possible to achieve this with galaxy tools. I've heard of
> galaxy tools but never made one so I don;t know what is involved.
> Failing that would i be able to use the biomart plugin to access my server if
> I had a local installation of galaxy
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
Greg Von Kuster
Galaxy Development Team
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: