Thanks for your help Dan but I’m still having the same problem. I explain you my advance:

-I have configured our local galaxy installation to an Apache proxy installation .

-Now we can access to galaxy url like http://IPdomain/galaxy

-When I click to display with IGV from a bam file it seems to work ok (It loads the bam file to IGV) but If I change the genome position in IGV it breaks and shows me the error msg:

ERROR [2012-12-03 14:15:42,776]  [CachingQueryReader.java:392] [pool-1-thread-2]  Error loading alignment data

net.sf.samtools.FileTruncatedException: Premature end of file

                at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:359)

                at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)

                at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)

is that a galaxy configuration  problem or IGV problem? I don’t understand because if I try to download first the bam file and then loading into IGV manually and If I change the genome position it works.

Thanks,

Joan

De: Daniel Blankenberg [mailto:dan@bx.psu.edu]
Enviado el: lunes, 26 de noviembre de 2012 17:54
Para: PROTASIO, JOAN (IDIBAPS)
CC: galaxy-dev@lists.bx.psu.edu
Asunto: Re: [galaxy-dev] Galaxy & IGV display error

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, <PROTASIO@clinic.ub.es> <PROTASIO@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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