Peter,
Thanks for explaining this alternate Galaxy site!

Archauha1,
You could also check the Tool Shed to see if they or anyone else has submitted a Galaxy wrapped version of the tool(s). And as Peter suggested, you could ask them to submit them. Once the tools are there (or shared with you directly), then you can set up a local or cloud Galaxy instance, add in the tools, and run your analysis.

Some info links:
http://galaxyproject.org/wiki/Big%20Picture/Choices
http://galaxyproject.org/wiki/Tool%20Shed
http://galaxyproject.org/wiki/Public%20Galaxy%20Servers

Best wishes for your project,

Jen
Galaxy team

On 11/14/11 2:24 PM, Peter Cock wrote:
On Mon, Nov 14, 2011 at 10:08 PM, Chauhan, Archana<achau...@utk.edu>  wrote:
Dear Sir/Madam,

                         I am registered with galaxy
http://main.g2.bx.psu.edu/. But I recently came across another link as
  https://galaxy.jgi-psf.org/ . This has some very good applications
especially w.r.t to the genome assembly (MIRA, velvet), microbial ecology
(Mothur etc) and Stats/Graphing Tools. Overall this links seems much better
than the Main galaxy and fulfils the general aspirations of a user. Is this
link subscribed JGI and its collaborators OR any one can be a part of it. Is
there any version of galaxy server wherein we can have these applications
available for public use. Thank you.


Tools like MIRA and Velvet can be extremely demanding to
run, so are "dangerous"/expensive to offer on a public Galaxy.

I don't know who exactly runs https://galaxy.jgi-psf.org/
and if they intend it to be available for external usage.

I wrote the MIRA wrapper for our in house use with viral
genomes (small enough not to be a big computational load)
and published it on the Galaxy toolshed for others to use
too in their own Galaxy servers. It is nice to see it being
used on https://galaxy.jgi-psf.org/ and it looks like they
have a pretty powerful cluster with big memory machines
with 500GB of RAM, which should cope with many MIRA
work loads.

If you have a local Galaxy at your department/institute then
try asking them if they can install this and other tools of
interest for you.

Regards,

Peter

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http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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/

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