Hello,
There are many ways to use Galaxy, and the tools offered/available in
each is often a choice made by the group hosting the instance (not the
version of the underlying code base):
http://wiki.galaxyproject.org/Big%20Picture/Choices
Wrappers for this tool are available from the tool shed:
http://toolshed.g2.bx.psu.edu/
This tool and any of the others in the tool shed are intended to run in
the latest Galaxy distribution. To get started with a local or cloud
instance, please see:
http://getgalaxy.org
Tools are often submitted by public contributors as donated work to the
community, so if you run into problems, the first place to start is to
contact the repository authors. The repository will note contact
information.
And you are correct, the public Main Galaxy instance
(http://main.g2.bx.psu.edu, aka "usegalaxy.org") does not host this
tool, but the version of Galaxy is not a factor. Some tools are hosted
on the public site and others are better suited for local/cloud use due
to resource or other reasons.
There are also other public Galaxy instances that may be of interest to
you. These can be explored to see if the tools or services offered fit
your needs. This wiki lists the sites known to us:
http://wiki.galaxyproject.org/PublicGalaxyServers
Concerning Cuffdiff - the public server has been very busy. If your jobs
are in a grey "waiting to run" state, the best strategy is to leave
these alone until they process. If any have ended in what appears to be
a cluster failure (this can occur occasionally during peak usage times),
then at least one re-run is recommended, and if problems continue that
you cannot diagnose, please submit a bug report and we can provide some
feedback (leaving all inputs/outputs undeleted). While queuing jobs, it
is important to not delete and then restart them, as this effectively
moves them back to the end of the processing queue. If you jobs are
urgent, then a local or cloud instance is recommended.
Hopefully this helps to clarify how the tools work!
Take care,
Jen
Galaxy team
On 1/29/13 2:55 PM, Ben Ben wrote:
Hi All,
Could anyone tell *Which Version Galaxy* has the function to run DESeq
(determine differentially expressed transcripts from read alignments)?
Any alternative?
As far as I know, *Penn State Version* doesn't integrate the DESeq
function.*And Cuffdiff seems stop working in Penn State *
Thanks very much for the response!!
Best wishes,
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
