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] wrote: > > 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]<javascript:> > > 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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> 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. 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.
