Davide,
Yes you are correct, a few reads from the bam file are showing up on chr10, from about 80,000 - 300,000, no other chr appear to have reads.  Well that explains the data retrieval issue and seeing data come from the web servers to ucsc.  It doesn't explain why no where else is displayed.  Is the entire file content being sent to ucsc with every request rather than the particular chunk to be displayed, so we are just hitting a ucsc data limit?  How could that be accessed?

I took a look at the previous thread at: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002691.html but I didn't see a solution as part of it. 

My apache is not forcing authentication, galaxy is supplying data to ucsc, some of the data is getting there for display.  The same file when loaded through our local http server for display at ucsc works normally, so the file is functional.  The same file loaded to the public galaxy server is functional, so public galaxy can provide the data properly. 

The galaxy build is from the current dist build and python is 2.5.

Are there any ideas what I have missed to get ucsc to display my bam files properly?
Thanks
Terry



On 6/18/2010 12:14 PM, Davide Cittaro wrote:
Hi there, I think we should join to find out what's going on... I have the very same issue. Can you check if you can display at least some thousands of reads at the beginning of chromosome 10 (or the fist chr in your BAM file anyway)?

d
On Jun 18, 2010, at 5:19 PM, Terrence Barrette wrote:

Hi,
I can't see the data at ucsc when I upload a bam file and try to display it.
The track arrives at ucsc.
I see GET /display_application/... and 200 and bytes in the httpd/access_log
I see GET /display_application/... in the paster.log
But I don't see the seq reads at the ucsc browser.

Some background information:
I am setting up our local galaxy server.
The server is redhat 5.
The IP is external and whether firewall is up or down is immaterial in the behavior.
The galaxy install is running at localhost:8080.
There is the default redhat apache running in front of galaxy with the rewrite rules enabled for static and all traffic to port 80.
Apache security is not enabled (yet).
The dedicated galaxy user and group is running galaxy.

Thanks,
Terry






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