[galaxy-dev] external ucsc link not working for BAM

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[galaxy-dev] external ucsc link not working for BAM

Davide Cittaro
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


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
*/




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Re: [galaxy-dev] external ucsc link not working for BAM

Nate Coraor (nate@bx.psu.edu)
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/917af94b51aeccc8/ucsc_bigWig/campus/30e4001c132619b4/param/track
>
> 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: [hidden email]
> <mailto:[hidden email]>
> */
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> galaxy-dev mailing list
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Re: [galaxy-dev] external ucsc link not working for BAM

Davide Cittaro

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
*/




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Re: [galaxy-dev] external ucsc link not working for BAM

Nate Coraor (nate@bx.psu.edu)
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
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Re: [galaxy-dev] external ucsc link not working for BAM

Davide Cittaro

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 "[hidden email]"
        </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
*/




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Re: [galaxy-dev] external ucsc link not working for BAM

Nate Coraor (nate@bx.psu.edu)
Davide Cittaro wrote:

> A (insecure?) workarond in apache configuration:
>
>
>         <LocationMatch /display_application >
>                 Satisfy any
>                 Order deny,allow
>                 Allow from XXXXXXX
>                 RequestHeader set REMOTE_USER
> "[hidden email] <mailto:[hidden email]>"
>         </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: [hidden email]
> <mailto:[hidden email]>
> */
>
>
>

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Re: [galaxy-dev] external ucsc link not working for BAM

Davide Cittaro

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 "[hidden email] <[hidden email]>"
       </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: [hidden email] <[hidden email]>
*/


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/




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