Dave, As far as I know the HPC does not have Galazy installed.
Best Robert M Jones On Tuesday, August 27, 2013 1:38:03 PM UTC-7, Dave Trudgian wrote: > > Robert, > > Do you know if any of the HPC systems have Galaxy installed? If they do > then maybe you could try to persuade sysadmins to install protK, which > allows TPP tools to be used from Galaxy: > > https://bitbucket.org/iracooke/protk > > There's also the galaxy-p project http://getgalaxyp.org/ but it needs a > ton of stuff to be installed on the cluster, which I'd guess most HPC > groups would not want to install. > > DT > > > On Tuesday, August 27, 2013 1:31:20 PM UTC-5, Robert Jones wrote: >> >> Joe, >> >> Awesome! Thank you so much! I'll give this a try today. >> >> Best, >> >> Robert M Jones >> >> On Monday, August 26, 2013 1:14:36 PM UTC-7, [email protected]: >>> >>> Robert, >>> >>> The bad news is that we haven't incorporated any logic in the Petunia >>> web interface of TPP to interact with a cluster system. Most users at this >>> level have been using the command line. Though we've been recently talking >>> about developing this. >>> >>> The good news though is I have some scripts that could be a good >>> starting point for you. They're simple scripts that wrap various search >>> engines to submit the jobs to a cluster. They're written for Sun Grid >>> Engine (SGE), but should be easily adapted for PBS (and in fact the >>> original versions were written for PBS). They're just simple shell scripts >>> that are intended to be copied and modified as needed. You'll find them in >>> sourceforge, at: >>> >>> >>> https://sourceforge.net/p/sashimi/code/6271/tree/trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/ >>> >>> I'm afraid installing/configuring them doesn't come with any >>> documentation. But basically just copy the qtandem, qcomet, etc scripts >>> along with the qgrid_functions script into a bin/ directory that's in your >>> PATH. Then open each up and change the locations to match how your system >>> is configured. You'll need to look at the PBS documentation as some of the >>> SGE directives at the top of the files won't work with PBS. >>> >>> -Joe >>> >>> >>> >>> On Mon, Aug 26, 2013 at 11:35 AM, Robert Jones <[email protected]>wrote: >>> >>>> Joe, >>>> >>>> Thanks for your prompt reply! As far as I know we are using a batch >>>> system since we submit jobs to a PBS. Since my knowledge of the HPC is >>>> sadly limited I attached a few links to the website that hopefully do a >>>> better job of explaining it than I could. >>>> >>>> >>>> http://rc2.webhost.uits.arizona.edu/hpc-htc/using-the-systems/overview-system-components >>>> http://rc2.webhost.uits.arizona.edu/hpc-htc/computing-systems >>>> >>>> And to answer you latter question we are using a Linux operating system >>>> allow we do have access to parallels and soon to a high powered PC >>>> >>>> Best, >>>> >>>> Robert M Jones >>>> >>>> >>>> >>>> On Friday, August 23, 2013 10:05:16 AM UTC-7, >>>> [email protected]: >>>> >>>>> Hi Robert, >>>>> >>>>> I'm happy to help out as I've been managing the execution of TPP on >>>>> our cluster here at ISB. How is your HPC setup? Are you using a batch >>>>> job >>>>> system such as Sun Grid Engine? And what Operating System are you using? >>>>> >>>>> Linux? >>>>> >>>>> -Joe >>>>> >>>>> >>>>> On Thu, Aug 22, 2013 at 2:53 PM, Robert Jones <[email protected]>wrote: >>>>> >>>>>> Hi All, >>>>>> >>>>>> I'm very new to using the TPP and the command line but in spite of >>>>>> that I have been tasked with managing the TPP on our local HPC. This can >>>>>> only be done through command line as far as I know so I was wondering if >>>>>> someone could point me in the direction of a comprehensive TPP command >>>>>> line >>>>>> tutorial to help get me started. Also, I'm curious if there is a way in >>>>>> which I could use the local TPP GUI on my computer but have the >>>>>> processing >>>>>> exported to the HPC. Thank you so much for any information you can give, >>>>>> I'm looking forward to using this software! >>>>>> >>>>>> Best, >>>>>> >>>>>> Robert M Jones >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "spctools-discuss" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to spctools-discu...@**googlegroups.com. >>>>>> To post to this group, send email to spctools...@googlegroups.**com. >>>>>> >>>>>> Visit this group at >>>>>> http://groups.google.com/**group/spctools-discuss<http://groups.google.com/group/spctools-discuss> >>>>>> . >>>>>> For more options, visit >>>>>> https://groups.google.com/**groups/opt_out<https://groups.google.com/groups/opt_out> >>>>>> . >>>>>> >>>>> >>>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "spctools-discuss" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> To post to this group, send email to [email protected]. >>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>> For more options, visit https://groups.google.com/groups/opt_out. >>>> >>> >>> -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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