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Old 04-23-2012, 03:58 AM   #1
qnc
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Default Trouble UpLoading BAM file to Galaxy

Hi I have been trying to upload this bam file

http://slm22.ioo.ucl.ac.uk/~qncwork/Vanita-Ori.bam

Which is located on this page
http://slm22.ioo.ucl.ac.uk/~qncwork/

All I get is:
"http://slm22.ioo.ucl.ac.uk/~qncwork/Vanita-Ori.bam
An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection.
error
format: bam, database: hg19
Info: Unable to fetch http://slm22.ioo.ucl.ac.uk/~qncwork/Vanita-Ori.bam
[Errno socket error] [Errno 110] Connection timed out"


I am happy to try UCSC but wanted to get a Variant's file from it to pass in Seatle Seq or something similar.

Then ultimately wanted to map any likely changes on UCSC with a MAF file.

But happy to look at the first stage which is getting BAM files uploaded.

Happy to look at other BAM analysis tools as well.

Can anyone help?
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Old 04-23-2012, 04:09 AM   #2
GenoMax
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The problem may be on your end. I can't access the file from the link you have provided for the bam file. Perhaps the firewall on your machine is preventing file access from outside.

Last edited by GenoMax; 04-23-2012 at 04:13 AM.
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Old 04-23-2012, 04:16 AM   #3
qnc
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Looking at other threads it might be a fire wall problem.

Is there any other site to host BAM and other large files on?

One without download restrictions?

Will check on the UCL Firewall status etc...

Thanks
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Old 04-23-2012, 04:24 AM   #4
GenoMax
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If this is sensitive/patient research data then you should consider setting up a local instance of galaxy rather that using the main galaxy site.

I am sure you have seen the disclaimer on the galaxy site about protected research data but just in case ....
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