I'm not Jen obviously, but I can maybe help a little. First let me
don't have a Galaxy install and am not even a novice yet, but I do get
question a lot. Here are some options
(1) if the Galaxy files are reachable by URL (http or ftp) you can
"File > Load from URL" and type in the URL to the bam (or other
file type). If its a bam file it will expect to find the index at
<bam url="">.bai. It won't download the whole file just the portion being
(2) you can drag & drop hyperlinks to files onto a running IGV as
(3) its possible to configure IGV as a viewer for bam files with a
XML. Regarding the 3rd option several people have done this by using
igv .jnlp file as a template and doing some galaxy magic to generate a
complete jnlp with the "argument" elements to the bam file inserted.
think there is such a file in the "toolshed". While this works
an easier way, we host a php file that does this for you. An
follows. You should be able to take the UCSC configuration example
modify it to use the IGV url below, the pattern and arguments are
The above option launches a new IGV instance on the file. There is a
second option which loads bams into an already running IGV. The xml I
seen for that, which I think is in the toolshed, is fine.
Finally there is a limitation with the above technique in that the
argument must be one of the IGV recognized ones. I'm testing code
will permit this argument to be a URL to any samtools indexed (.fai)
file. It will be released shortly.
-- Jim (IGV developer)