Thanks Dan. I'll pull in the change on Monday (don't have access to our instance atm). 

On a related note which might be of interest to Brad, can I suggest that $GALAXY_ROOT/display_applications/igv/[bam/sam].xml include:

&name=${bam_file.name}

at the the end of the url generated for IGV viewing. At the moment, pulling down galaxy bam files generates uninformative track names. Adding the 'name' parameter to the url will copy the name of the dataset in galaxy to the name of the track. If you're pulling in many bam tracks into IGV, this tiny change makes everything a *lot* easier.

See http://youtu.be/88MKSHHYHjc for an example.

Thanks for the great work, Galaxy devs.

-r

On Sat, Jun 23, 2012 at 1:32 AM, Daniel Blankenberg <dan@bx.psu.edu> wrote:

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_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_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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