Hi Tao,

I'm not Jen obviously, but I can maybe help a little.   First let me say I don't have a Galaxy install and am not even a novice yet, but I do get this question a lot.  Here are some options 

(1) if the Galaxy files are reachable by URL (http or ftp) you can just use "File > Load from URL"  and type in the URL to the bam (or other supported 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 viewed.  

(2) you can drag & drop hyperlinks to files onto a running IGV as well,  the the link is a direct link (not javascript or a formsubmission, etc), 

(3) its possible to configure IGV as a viewer for bam files with a little XML.  Regarding the 3rd option several people have done this by using the 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.   I think there is such a file in the "toolshed".    While this works there is an easier way,  we host a php file that does this for you.   An example URL follows.   You should be able to take the UCSC configuration example and modify it to use the IGV url below,  the pattern and arguments are almost the same

http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=http://www.broadinstitute.org/igvdata/1KG/pilot2Bams/NA12878.SLX.bam&genome=hg18&locus=chr1:64,098,103-64,098,175

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 have seen for that, which I think is in the toolshed,  is fine.

Finally there is a limitation with the above technique in that the genome argument must be one of the IGV recognized ones.   I'm testing code now that will permit this argument to be a URL to any samtools indexed (.fai) fasta file.   It will be released shortly.

-- Jim  (IGV developer)


On Fri, Aug 26, 2011 at 7:23 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:
===> Please use "Reply All" when responding to this email! <===




Hi Jen, is anyway I can directly load the analyzed data from galaxy to
IGV (Integrative genome viewer) without downloading data to my computer
first?

Thanks,


tao


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