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,
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.
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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: