Hi Rob,

Changeset 7300:f197c4346cc4, which is currently available in galaxy-central, 
should allow the external display applications to work when require_login = 
True, thanks for reporting this error. Please let us know if you encounter 
additional issues.


Thanks for using Galaxy,

Dan


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 
> http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/aaaaaaaaaaaaaaaa/data/galaxy_e2132aef71b11dbf.bam,
>  galaxy redirects to the login page.
> 
> I tried to remove the authentication requiements with the apache config (as 
> per 
> https://sites.google.com/site/princetonhtseq/tutorials/visualization-with-galaxy-and-igv/igv-as-a-display-application-in-galaxy):
> 
>         <LocationMatch display_application/[a-zA-Z0-9]+/igv.*>
>                 RequestHeader set REMOTE_USER igv_disp...@example.org
>                 Satisfy Any
>                 Order deny,allow
>                 Allow from all
>         </LocationMatch>
> 
> 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.
> -r
> 
> 
> 
> On Fri, Jun 22, 2012 at 2:16 PM, Rob Syme <rob.s...@gmail.com> wrote:
> Sorry, the subject should read "mistakenly routed to root". The question 
> still stands.
> -r
> 
> 
> On Fri, Jun 22, 2012 at 2:10 PM, Rob Syme <rob.s...@gmail.com> wrote:
> Galaxy type: local
> 
> I'm trying to get IGV to download files served from the galaxy instance 
> through "display_application". 
> When IGV makes a request for the BAM file, it is re-routed to root like so:
> 
> wget 
> http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam
> --2012-06-22 13:58:00--  
> http://example.org/galaxy/display_application/e2132aef71b11dbf/igv_bam/local_default/cc7ba224ab9e7b70/data/galaxy_e2132aef71b11dbf.bam
> Connecting to example.org:80... connected.
> HTTP request sent, awaiting response... 302 Found
> Location: 
> /galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf
>  [following]
> --2012-06-22 13:58:00--  
> http://example.org/galaxy/root?app_action=data&user_id=cc7ba224ab9e7b70&app_name=igv_bam&link_name=local_default&action_param=galaxy_e2132aef71b11dbf.bam&dataset_id=e2132aef71b11dbf
> Reusing existing connection to 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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