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. 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.
