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..., 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-ga... ): <LocationMatch display_application/[a-zA-Z0-9]+/igv.*> RequestHeader set REMOTE_USER igv_display@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.syme@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.syme@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... --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