Re: [galaxy-dev] Galaxy and ENCODE
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 ___ 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/
Re: [galaxy-dev] Galaxy and ENCODE
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 ___ 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/
Re: [galaxy-dev] Galaxy and ENCODE
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 ___ 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/
