Devesh, I would imagine your best bet then would be to download the TPP source, compile it on your Linux system then just copy the executable of the programs that you wish to use.
The source is available at http://sourceforge.net/projects/sashimi/files/latest/download?source=files -Joe On Sun, Sep 15, 2013 at 11:35 PM, devesh chourasiya <devesh...@gmail.com>wrote: > Hi All, > > We are trying to create work-flow based on TPP using resources of iPlant ( > http://www.iplantcollaborative.org/ ) and XSEDE (https://www.xsede.org/). > To implement this we need to create apps ( iPlant specific term for any > tool ) for each of the tool used in TPP and then we can call these apps in > order to generate workflow. Please let us location from where we can > download each of these tools separately for linux, instead of a > consolidated TPP installer. These tools will be installed on remote server > and will be invoked using RESTful APIs. > > We want this workflow to be command line based only instead of GUI > support. > > Devesh > > > On Wednesday, August 28, 2013 12:25:23 PM UTC-7, Robert Jones wrote: >> >> 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<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, >>>> jsl...@systemsbiology.orgwrote: >>>>> >>>>> 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/<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 >>>>> <magicai...@gmail.com>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/using-the-systems/overview-system-components> >>>>>> http://rc2.webhost.uits.**arizona.edu/hpc-htc/computing-**systems<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, >>>>>> jsl...@systemsbiology.org wrote: >>>>>> >>>>>>> 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 >>>>>>> <magicai...@gmail.com>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/**grou** >>>>>>>> ps/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 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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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