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/m... 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-chapm...
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
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?
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-June/002802.html
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 */
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
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 galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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@lists.galaxyproject.org
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Brad Chapman -
Davide Cittaro -
Nate Coraor -
Stephen Taylor