On 11/19/12 11:21 AM, "James Taylor" <
james@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 <
HWillis@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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