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).

On Jan 14, 2012, at 10:09 PM, bt.microzhang@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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