It's an excellent idea . Does anybody have a document around the work
package ? I'm sure that many people will be happy to participate.

Victoria

On Mon, Nov 19, 2012 at 8:03 PM, Scooter Willis <hwil...@scripps.edu> wrote:

> Thank you for the clarification. Would be an interesting project for a
> Galaxy hackathon to move over the ENCODE tools/workflow to run in Galaxy.
>
> On 11/19/12 11:21 AM, "James Taylor" <ja...@jamestaylor.org> wrote:
>
> >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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