Stephen Taylor wrote:

Hi,

I am trying to display some data in the main public UCSC genome browser via our local Galaxy instance (based on http://bitbucket.org/galaxy/galaxy-central/wiki/ExternalDisplayApplications/... and http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy). I removed the strip_https="True" form the bigwig.xml in display_applications/ucsc, because we only support https on our server and it seems UCSC does support retrieving data over https.

Hi Stephen, If you're still working on this issue, I've just removed the hack which was in place for UCSC, since it did not support https in the past. This is in changeset 4788:8dce5263b43f, which you can get by pulling directly from our in-development repository at: http://bitbucket.org/galaxy/galaxy-central Or by waiting for our next stable release, which should hopefully be out later this week. Please make sure you're setting X-URL-SCHEME as described in the Apache proxy instructions and let us know if this is working for you: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy Thanks, --nate

When I try to view a bigWig file in Galaxy (that I have tested works via https URL directly in UCSC):

"xxxx.bigwig is not a chromosome id r-tree index file" in a UCSC panel at the UCSC site.

or

"udc couldn't read 4 bytes from xxxx.bigwig, did read 0"

(where xxxx = https URL)

If I then add in my machine to the apache conf and try and see download xxxx.bigwig via a web browser I get:

"Access to Galaxy is denied

Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server. This is generally due to a misconfiguration in the upstream server.

Please contact your local Galaxy administrator."

I was assuming setting deny/allow would negate the need for a password on these files when connected to by approved servers, but perhaps I am doing something wrong here?

Another question I have is should I use

<Location "/display_as"> (as per http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy)

or

<Location "/display_application">

since their doesn't seem to be display_as in the URL. I use the same deny/allow for both to be on the safe side:

<Location "/display_application"> Satisfy Any Order Deny,Allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location>

<Location "/display_as"> Satisfy Any Order Deny,Allow Deny from all Allow from hgw1.cse.ucsc.edu Allow from hgw2.cse.ucsc.edu Allow from hgw3.cse.ucsc.edu Allow from hgw4.cse.ucsc.edu Allow from hgw5.cse.ucsc.edu Allow from hgw6.cse.ucsc.edu Allow from hgw7.cse.ucsc.edu Allow from hgw8.cse.ucsc.edu </Location>

Any ideas would be much appreciated!

Thanks in advance,

Steve

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