One other little nugget. If Galaxy is externally authenticated, I
can't display custom tracks on my local mirror. It timed out when I tried to display
them on the main UCSC site. I guess this is because the bed files are behind the
authentication, right? Maybe I should rethink this external authentication...
It's possible to work around it if you're willing to give up a bit of
security. See the "Display at UCSC" section of ApacheProxy:
You'll have to add your own mirror to remoteuser.py as well (this list
of servers should not be hardcoded but we haven't gotten to fixing that
On Nov 2, 2010, at 3:09 PM, Nate Coraor wrote:
David Hoover wrote:
> Right, and a few other things. I had to change the name and id of the tool in the
new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as
well. The new id was added to the list of [galaxy:tool_runners] with local:/// as well.
Ah yes, a few more steps than I had. I'll get this all into the wiki.
The data source tools can run on the cluster if your cluster nodes are
able to initiate connections out to their sources (so NAT is okay).
The upload tool can also run on the cluster, you just have to set $TEMP
to somewhere in a filesystem shared between the Galaxy server and the
cluster (e.g. galaxy_dist/database/tmp/) in the environment in which
Galaxy is started.
> A little roundabout, but doable. Thanks for your help.
> On Nov 2, 2010, at 2:35 PM, Nate Coraor wrote:
> Victor Ruotti wrote:
>> Hi David,
>> This might help you.
> Sorry, this information is a bit outdated. There is a more recent page
> that covers writing display applications, but it's written from the
> perspective of adding entirely new display applications rather than
> linking to an existing browser:
> The relevant information is that that the site should be given a name
> and added to:
> Once done, that name should be added to the parameter
> 'ucsc_display_sites' in universe_wsgi.ini. This will enable your
> browser for the "display at ..." links under compatible file types of
> data in your history.
> To add your local mirror as a data source tool, you'll need to make a
> copy of:
> And change the URL in the <inputs> tag to point to your local browser.
> Once this is done, add the path to your new XML file to 'tool_conf.xml'
> and restart Galaxy.
> I'll work on getting this information added to the wiki.
>> On Nov 2, 2010, at 1:10 PM, David Hoover wrote:
>>> I modified universe_wsgi.ini and the files in ~/tool-data/shared/ucsc, then
restarted galaxy, but it still downloads data from UCSC instead of the local mirror. Is
there something I missed?
>>> On Nov 2, 2010, at 1:31 PM, Victor Ruotti wrote:
>>> Hi David,
>>> For the table browser we set up here.
>>> biomart = local:///
>>> encode_db1 = local:///
>>> hbvar = local:///
>>> microbial_import1 = local:///
>>> ucsc_table_direct1 = http://localgenome.cgi-bin/hgTables
> This is not what this section is used for, in fact. The
> [galaxy:tool_runners] section of the config is used by the job
> dispatcher to determine whether the tool should run locally or on a
> cluster (and with what cluster parameters).
>>> ucsc_table_direct_archaea1 = local:///
>>> ucsc_table_direct_test1 = local:///
>>> upload1 = local:///
>>> For displaying the actual genome with bed files we changed the file.
>>> So it points to our local genome browser.
>>> Hope this helps.
>>> On Nov 2, 2010, at 12:23 PM, David Hoover wrote:
>>>> Is there any way of having Galaxy use a local mirror of the UCSC Genome
Browser instead of the main site? Is there a central config file somewhere that I can
just change genome.ucsc.edu
to something else?
>>>> David Hoover
>>>> Helix Systems Staff
>>>> galaxy-dev mailing list
>> galaxy-dev mailing list