Scooter,

The ENCODE VM which is available on Amazon Web Services and as a
downloadable VM[1] uses Galaxy's Cloudman component for managing
storage and compute resources. However, the Galaxy analysis interface
was not used.  All of the code for analysis performed in the ENCODE
integrated paper is included in the VM, however most of the components
are not exposed as Galaxy tools or workflows. It would definitely be
possible to do so if you are interested, however any given analysis
may not have been built with reuse on different datasets in mind.


Thanks!

[1] http://encodeproject.org/ENCODE/integrativeAnalysis/VM/

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Sun, Nov 18, 2012 at 10:29 AM, Scooter Willis <hwil...@scripps.edu> wrote:
> I found out about Galaxy based on the ENCODE project making a big deal about
> packaging the software they used on a CD and available for download. I
> misplaced the CD and following some link on an ENCODE/Nature web site found
> Galaxy. What I haven't found is any public workflows that would indicate
> this is what ENCODE was doing to call SNPs or assemble RNAseq data. It
> appears that number of public workflows are minimal. Maybe I am not pointing
> to the correct repository. Can someone provide some guidance on ENCODE use
> of Galaxy and where I can find ENCODE workflows? I seem to remember the
> ENCODE Nature publication having a CD but never looked at it. If this was
> the case did ENCODE package a vmware'ish version of Galaxy on the CD?
>
> Thanks
>
> Scooter
>
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