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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