Hi Joan,

For IGV and most external displays that work on BAM and other larger seekable 
file formats (bigwig, bigbed, etc.) you'll need to use and configure a proxy 
server for your local Galaxy instance that provides byte-range request 
capabilities, such as nginx 
(http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy) or 
apache (http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy). 


Thanks for using Galaxy,

Dan


On Nov 26, 2012, at 6:11 AM, <prota...@clinic.ub.es> <prota...@clinic.ub.es> 
wrote:

> Hi all,
>  
> I’m having  problems when I click to visualize one BAM file from galaxy to 
> IGV version 2.1.24. I’ve tried the local and also the web display options  
> but I have the same problem. I have tried also to download first the bam file 
> from galaxy and then loading into IGV manually and it works. I also have 
> tried to modify the .jnlp generated but it does not work.
>  
> IGV shows the next error message:
>  
> ERROR [2012-11-26 11:44:54,591]  [IGV.java:1555] [pool-1-thread-1]  
> net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in 
> readmode; streamed file (filename not available)
> ERROR [2012-11-26 11:44:54,592]  [IGV.java:1494] [pool-1-thread-1]  Error 
> loading tracks
> org.broad.igv.exceptions.DataLoadException: An error occurred while 
> accessing:   
> http://172.21.104.21:8080/display_application/9e23127bd2c9a880/igv_bam/web_link_main/8d9bcc17f9fede63/data/galaxy_9e23127bd2c9a880.bam<br>Premature
>  EOF; BinaryCodec in readmode; streamed file (filename not available)
>  
> Thanks for your help.
>  
>  
> Joan Protasio,  Bioinformatician & Software Engineer
> Bioinformatics Platform 
> August Pi i Sunyer Biomedical Research Institute (IDIBAPS)
> C/ Rosselló 153, Barcelona
> http://bioinformatics.fcrb.es
> +34  93 227 54 00 ext. 4522
>  
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