Hi again, I've done with plugging our local UCSC mirror into galaxy. I'm able to view most of the data except for BAM and bigWig files. I'm adding bigWig as new datatype as we mostly work with that. Besides the fact I'm not able to sniff properly the bigWig data type (but I still can define the type at import time), I'm not able to view in UCSC. Essentially I've copied the ucsc/bam.xml file and edited to enable bigWig tracks. The problem now is that BAM (or bigWig) can't be viewed by the UCSC because of authentication issues :-( The UCSC mirrors says that this address
http://host001.instruments.ifom-ieo-campus.it:8080/display_application/917af...
generated by galaxy cannot be viewed (auth required)... Indeed this URL format differs from the one defined for bed files which is in the form of HOST:PORT/root/display_as?PARAMS. The latter has a special configuration in my apache conf file (as suggested by Nate and others), but the same conf for
<Location /display_application>
doesn't work (I believe this depends on /lib/galaxy/web/framework/middleware/remoteuser.py implementation).
d /* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Davide Cittaro wrote:
Hi again, I've done with plugging our local UCSC mirror into galaxy. I'm able to view most of the data except for BAM and bigWig files. I'm adding bigWig as new datatype as we mostly work with that. Besides the fact I'm not able to sniff properly the bigWig data type (but I still can define the type at import time), I'm not able to view in UCSC. Essentially I've copied the ucsc/bam.xml file and edited to enable bigWig tracks. The problem now is that BAM (or bigWig) can't be viewed by the UCSC because of authentication issues :-( The UCSC mirrors says that this address
http://host001.instruments.ifom-ieo-campus.it:8080/display_application/917af...
generated by galaxy cannot be viewed (auth required)... Indeed this URL format differs from the one defined for bed files which is in the form of HOST:PORT/root/display_as?PARAMS. The latter has a special configuration in my apache conf file (as suggested by Nate and others), but the same conf for
<Location /display_application>
doesn't work (I believe this depends on /lib/galaxy/web/framework/middleware/remoteuser.py implementation).
You're correct, this new-style display application path hasn't been added to the "display at" loophole. This should probably be added to the ticket about hardcoded UCSC servers so we can overhaul it all at once.
--nate
d /* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On May 26, 2010, at 3:34 PM, Nate Coraor wrote:
doesn't work (I believe this depends on /lib/galaxy/web/framework/middleware/remoteuser.py implementation).
You're correct, this new-style display application path hasn't been added to the "display at" loophole. This should probably be added to the ticket about hardcoded UCSC servers so we can overhaul it all at once.
Just another question: how do you enable viewing of BAM files from your galaxy to the cse.edu ucsc site (given that the "display_as" rule in apache is not enough)?
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Davide Cittaro wrote:
Just another question: how do you enable viewing of BAM files from your galaxy to the cse.edu http://cse.edu ucsc site (given that the "display_as" rule in apache is not enough)?
Our Galaxy site isn't behind authorization, so no extra rules are necessary.
--nate
On May 26, 2010, at 9:03 PM, Nate Coraor wrote:
Davide Cittaro wrote:
Just another question: how do you enable viewing of BAM files from your galaxy to the cse.edu http://cse.edu ucsc site (given that the "display_as" rule in apache is not enough)?
Our Galaxy site isn't behind authorization, so no extra rules are necessary.
A (insecure?) workarond in apache configuration:
<LocationMatch /display_application > Satisfy any Order deny,allow Allow from XXXXXXX RequestHeader set REMOTE_USER "ucsc_browser_display@example.org" </LocationMatch>
in XXX I have the definition for all the campus network.
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Davide Cittaro wrote:
A (insecure?) workarond in apache configuration:
<LocationMatch /display_application > Satisfy any Order deny,allow Allow from XXXXXXX RequestHeader set REMOTE_USER"ucsc_browser_display@example.org mailto:ucsc_browser_display@example.org" </LocationMatch>
in XXX I have the definition for all the campus network.
I recall that someone else (Ross?) was doing a similar thing (allowing access in Galaxy via a special UCSC user).
--nate
d
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
On May 28, 2010, at 2:57 PM, Nate Coraor wrote:
Davide Cittaro wrote:
A (insecure?) workarond in apache configuration: <LocationMatch /display_application > Satisfy any Order deny,allow Allow from XXXXXXX RequestHeader set REMOTE_USER "ucsc_browser_display@example.org mailto:ucsc_browser_display@example.org" </LocationMatch> in XXX I have the definition for all the campus network.
I recall that someone else (Ross?) was doing a similar thing (allowing access in Galaxy via a special UCSC user).
Also, in remoteuser.py there's a section in which a fake UCSC user is created on the fly for displaying tracks...
d
--nate
d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it mailto:davide.cittaro@ifom-ieo-campus.it */
/* Davide Cittaro
Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy
tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
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Nate Coraor