sysadmin help

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sysadmin help

Shrum, Donald C
Hi all,

I could use a little basic help.  I'm setting up a proof of concept galaxy server that will run in conjunction with our HPC here at FSU.  Ultimately this will serve as a template where we will allow some users to run galaxy on a VM and use it as a mechanism for submitting/managing jobs on our cluster.

I've installed Galaxy on a VM that mounts our HPC file system and managed to import an ecoli .fa file.

My plan was to run bowtie2 on our HPC.  
https://rcc.fsu.edu/software/bowtie2

Disclaimer... I'm a sysadmin and other than compiling software my knowledge in bioinformatics is sorely lacking ;)

I'm looking at the docs here  https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
I get a 404 for details on Torque - http://www.clusterresources.com/pages/products/torque-resource-manager.php 

Any help would be greatly appreciated.  Additionally, if my intended use for Galaxy seems out of the scope of what would be useful, please let me know.

Thanks,
Donny Shrum
FSU Research Computing Center
 


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Re: sysadmin help

Nate Coraor (nate@bx.psu.edu)
Hi Donny,

Thanks for the heads up about the broken link, I've fixed it. Other than that, are you running in to problems connecting Galaxy to your existing cluster?

--nate


On Tue, Jan 28, 2014 at 9:29 PM, Shrum, Donald C <[hidden email]> wrote:
Hi all,

I could use a little basic help.  I'm setting up a proof of concept galaxy server that will run in conjunction with our HPC here at FSU.  Ultimately this will serve as a template where we will allow some users to run galaxy on a VM and use it as a mechanism for submitting/managing jobs on our cluster.

I've installed Galaxy on a VM that mounts our HPC file system and managed to import an ecoli .fa file.

My plan was to run bowtie2 on our HPC.
https://rcc.fsu.edu/software/bowtie2

Disclaimer... I'm a sysadmin and other than compiling software my knowledge in bioinformatics is sorely lacking ;)

I'm looking at the docs here  https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
I get a 404 for details on Torque - http://www.clusterresources.com/pages/products/torque-resource-manager.php

Any help would be greatly appreciated.  Additionally, if my intended use for Galaxy seems out of the scope of what would be useful, please let me know.

Thanks,
Donny Shrum
FSU Research Computing Center



___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/