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. Regards, Archana Post-Doctoral Research Scholar, University of Tennesse Knoxville, USA
On Mon, Nov 14, 2011 at 10:08 PM, Chauhan, Archana <achauha1@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
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<achauha1@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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participants (3)
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Chauhan, Archana -
Jennifer Jackson -
Peter Cock