bigWig display at UCSC

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

bigWig display at UCSC

Brad Chapman
Hi all;
We're having trouble displaying BigWigFiles at UCSC and are getting
error messages from UCSC like:

http://main.g2.bx.psu.edu/display_application/238cdead8fb6f8fe/ucsc_bigwig/main/e2f1101c6342a137/data/galaxy_238cdead8fb6f8fe.bigwig is not a chromosome id r-tree index file

I see the same issue on Galaxy main, which can be replicated by
trying to view the test.bigwig file from this history:

http://main.g2.bx.psu.edu/u/Brad%20Chapman/h/imported-test-history-for-chapman

We noticed the problem after an upgrade to the latest galaxy-central
on Friday, but I haven't been able to track down any changes which
seem to be causing it. Other display types (BAM, regular wiggle)
work fine.

Does anyone know of recent changes to display applications which
might be causing this? Any directions to dig into would be
appreciated. Thanks much,

Brad
_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev
Reply | Threaded
Open this post in threaded view
|

Re: bigWig display at UCSC

Davide Cittaro

On Nov 29, 2010, at 8:07 PM, Brad Chapman wrote:

Does anyone know of recent changes to display applications which
might be causing this? Any directions to dig into would be
appreciated. Thanks much,


Is this helpful?


d

/*
Davide Cittaro

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

tel.: +39(02)574303007
*/




_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev
Reply | Threaded
Open this post in threaded view
|

Re: bigWig display at UCSC

Brad Chapman
Hi all;

[bigWig display problems]
> > Does anyone know of recent changes to display applications which
> > might be causing this? Any directions to dig into would be
> > appreciated. Thanks much,

Davide, thanks for the pointer to that discussion. This was a
big help to get me looking the right direction by staring at the
headers.

The problem is due to adding 'string_as_bool' to the nginx
configuration parameters in this changeset:

http://bitbucket.org/galaxy/galaxy-central/changeset/70ac3aef6dab

All of the nginx paramters in universe_wsgi.ini are string values, not
true/false like apache, so this results in paste serving out files
instead of nginx. Paste and bigWig access don't play nicely together,
resulting in the failure to display them. This four line fix will get
things working again:

http://bitbucket.org/chapmanb/galaxy-central/changeset/0b8fdb89ee64

Thanks,
Brad
_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev
Reply | Threaded
Open this post in threaded view
|

Re: bigWig display at UCSC

Nate Coraor (nate@bx.psu.edu)
Brad Chapman wrote:

> Hi all;
>
> [bigWig display problems]
> > > Does anyone know of recent changes to display applications which
> > > might be causing this? Any directions to dig into would be
> > > appreciated. Thanks much,
>
> Davide, thanks for the pointer to that discussion. This was a
> big help to get me looking the right direction by staring at the
> headers.
>
> The problem is due to adding 'string_as_bool' to the nginx
> configuration parameters in this changeset:
>
> http://bitbucket.org/galaxy/galaxy-central/changeset/70ac3aef6dab

I have no idea why I did that. ;)

> All of the nginx paramters in universe_wsgi.ini are string values, not
> true/false like apache, so this results in paste serving out files
> instead of nginx. Paste and bigWig access don't play nicely together,
> resulting in the failure to display them. This four line fix will get
> things working again:
>
> http://bitbucket.org/chapmanb/galaxy-central/changeset/0b8fdb89ee64

Thanks, committed back to galaxy-central.

--nate

>
> Thanks,
> Brad
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev
Reply | Threaded
Open this post in threaded view
|

Re: bigWig display at UCSC

Stephen Taylor
Hi,

>>
>> [bigWig display problems]
>>>> Does anyone know of recent changes to display applications which
>>>> might be causing this? Any directions to dig into would be
>>>> appreciated. Thanks much,
>> Davide, thanks for the pointer to that discussion. This was a
>> big help to get me looking the right direction by staring at the
>> headers.
>>
>> The problem is due to adding 'string_as_bool' to the nginx
>> configuration parameters in this changeset:
>>
>> http://bitbucket.org/galaxy/galaxy-central/changeset/70ac3aef6dab
>
> I have no idea why I did that. ;)
>
>> All of the nginx paramters in universe_wsgi.ini are string values, not
>> true/false like apache, so this results in paste serving out files
>> instead of nginx. Paste and bigWig access don't play nicely together,
>> resulting in the failure to display them. This four line fix will get
>> things working again:
>>
>> http://bitbucket.org/chapmanb/galaxy-central/changeset/0b8fdb89ee64
>
> Thanks, committed back to galaxy-central.
>

This was a very useful thread!

We are using Apache (rather than nginx) and setting

XSendFile On

andsetting

XSendFilePath<path>

in ssl.conf

Also added "apache_xsendfile = True" in {web|job}_universe_wsgi.ini

We can now view bigwig and bam files at UCSC.

Thanks for all the useful comments.

Steve

_______________________________________________
galaxy-dev mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-dev