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/Tutorial
> 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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