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:d...@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, <prota...@clinic.ub.es<mailto:prota...@clinic.ub.es>> <prota...@clinic.ub.es<mailto: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<http://bioinformatics.fcrb.es/> +34 93 227 54 00 ext. 4522 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
