While I have not yet added IGV for display, I would like to and I would also 
like to add tablet so I'm interested in how this plays out.
Hopefully someone more knowledgable will chime in.

Meanwhile, I'll try to help.  I think that the 302 redirect indicates that 
REMOTE_USER is not being set or is not beiing respected.

I think you have to enable external authentication in universe_wsgi.ini for 
REMOTE_USER to be respected by galaxy.

Assuming you do have external auth set up...

Can you actually log in to galaxy as 

I think you would need to either configure that user in galaxy or allow it to 
be automatically created (via allow_user_creation)
It might also be worth looking at remote_user_maildomain and try eliminating 
the @example.org

Another possibility:

are you sure that this url
is matched by <LocationMatch display_application/[a-zA-Z0-9]+/igv.*>

I don't know if a regex in a LocationMatch is implicitly left anchored.
 might be worth trying  /galaxy/display_application/...


On Jun 22, 2012, at 3:48 AM, Rob Syme wrote:

The problem seems to be in the lack of authentication by the request sent by 
IGV. The galaxy instance is set to require a username and password with 
"require_login = True" in universe_wsgi.ini, which means that when IGV attempts 
to download the BAM file at 
 galaxy redirects to the login page.

I tried to remove the authentication requiements with the apache config (as per 

        <LocationMatch display_application/[a-zA-Z0-9]+/igv.*>
                RequestHeader set REMOTE_USER 
                Satisfy Any
                Order deny,allow
                Allow from all

But it didn't help.
Commenting out the "require_login = True" line allows IGV to connect and 
download the bam file without issue.

I've now got IGV crashing when trying to access this BAM file, but that's 
probably a question for their list.

On Fri, Jun 22, 2012 at 2:16 PM, Rob Syme 
<rob.s...@gmail.com<mailto:rob.s...@gmail.com>> wrote:
Sorry, the subject should read "mistakenly routed to root". The question still 

On Fri, Jun 22, 2012 at 2:10 PM, Rob Syme 
<rob.s...@gmail.com<mailto:rob.s...@gmail.com>> wrote:
Galaxy type: local

I'm trying to get IGV to download files served from the galaxy instance through 
When IGV makes a request for the BAM file, it is re-routed to root like so:

--2012-06-22 13:58:00--  
Connecting to example.org<http://example.org/>:80... connected.
HTTP request sent, awaiting response... 302 Found
--2012-06-22 13:58:00--  
Reusing existing connection to example.org<http://example.org/>:80.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]
Saving to: 'galaxy_e2132aef71b11dbf.bam.1'

    [ <=>                                                                       
                                                      ] 27,581      --.-K/s   
in 0s

2012-06-22 13:58:00 (146 MB/s) - 'galaxy_e2132aef71b11dbf.bam.1' saved [27581]

Giving us a text/html page rather than the BAM file.

I see that I'm not the first person to run into this: 
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007901.html but I'm 
still not really sure how to solve the problem.

I'm no sysadmin, so my apache config skills are very patchy. My config is up at 
https://gist.github.com/2970592. Any help would be very much appreciated.

Rob Syme

PhD Student
Curtin University

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Brad Langhorst

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