Hi Dan, thanks for the response.   Does Galaxy index VCF files, for example with tabix of the "tribble" library?  IGV currently requires indexes for VCF files, mainly because the ones we generate here are huge.   This could be relaxed for smaller VCF files, and I have that on my list.

best,

Jim

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.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
___________________________________________________________
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/