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 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! > > > > 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 > >> > >> ___________________________________________________________ > >> 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: > >> > >> http://lists.bx.psu.edu/ > > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ >
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