Galaxy and ENCODE

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Galaxy and ENCODE

Scooter Willis-2
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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Re: Galaxy and ENCODE

James Taylor-2
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 <[hidden email]> 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/
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Re: Galaxy and ENCODE

Scooter Willis-2
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" <[hidden email]> 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 <[hidden email]>
>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/


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Re: Galaxy and ENCODE

Victoria D Bohler
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 <[hidden email]> 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" <[hidden email]> 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 <[hidden email]>
>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/


___________________________________________________________
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/