Hi Ming,

From Galaxy, you can currently view BAM and VCF (VCF is available in -central, 
but will be in the next -dist release) files within IGV.  To do this on a local 
set up, you will need to have your Galaxy instance behind a proxy (e.g. nginx 
or apache); this enables byte-range requests. In the datatypes_conf.xml file, 
make sure that '<display file="igv/bam.xml" />' and '<display 
file="igv/vcf.xml" />' are not commented out. Within Galaxy, your BAM or VCF 
file should have the dbkey set to a build that is configured to be viewable at 
IGV (see tool-data/shared/igv/igv_build_sites.txt).

Please let us know if we can provide additional assistance.


Thanks for using Galaxy,

Dan


On Jan 14, 2012, at 10:09 PM, bt.microzh...@gmail.com wrote:

> Hi Guys,
>     I am glad to hear form Jim Robinson that  exists some code could wrap IGV 
> as a Galaxy visualizer. Recently, i implemented local Galaxy instant and 
> wanted to integrate
> IGV as a visualizer. I'm looking forward your reply.
> 
> Regards,
> 
> Ming 
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