[kepler-users] Regarding Addition of tools

[Jianwu Wang]

Hi Pavan,

     I think it is probably because the R script in your R actor has 
some problems. If you want to make sure R is working with Kepler, you 
can try demo workflows at 
~/KeplerData/workflows/module/r-2.3.0/demos/R/, such as R_3D_Plot.xml.  
If you can run the demo workflows, it means R is working and your own R 
script has problems. Then you can try run R scripts directly in R and 
check its error.

     P.S.: please send your future questions directly to 
kepler-users at kepler-project.org, where you will get more prompt and 
comprehensive help.

Best wishes

Sincerely yours

Jianwu Wang, Ph.D.
jianwu at sdsc.edu
http://users.sdsc.edu/~jianwu/

Assistant Project Scientist
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.

On 9/17/12 12:23 AM, Pavan Kumar wrote:
> Dear Jianwu,
>
> Thanks for the prompt reply.
> I am able to use Kepler and can create a workflows.
> But for some workflows, I am getting the following error repeatedly.
>
> /ptolemy.kernel.util.IllegalActionException: R returned with value 1, 
> likely caused  by an error while executing the script/.
>
> I am sure R is properly installed and its path is also properly set.
> Is there any problem in R script. Please help me in this issue.
> Thanks in advance. Hope you will get back to me ASAP.
>
>
> On Fri, Sep 14, 2012 at 4:00 AM, Jianwu Wang <jianwu at sdsc.edu 
> <mailto:jianwu at sdsc.edu>> wrote:
>
>     Hi Pavan,
>
>         Please check Kepler user manual (Section 7.3 Job Submission),
>     which has detailed information about it. User manual can be found
>     at https://kepler-project.org/users/documentation.
>
>     Best wishes
>
>     Sincerely yours
>
>     Jianwu Wang, Ph.D.
>     jianwu at sdsc.edu  <mailto:jianwu at sdsc.edu>
>     http://users.sdsc.edu/~jianwu/  <http://users.sdsc.edu/%7Ejianwu/>
>
>     Assistant Project Scientist
>     Scientific Workflow Automation Technologies (SWAT) Laboratory
>     San Diego Supercomputer Center
>     University of California, San Diego
>     San Diego, CA, U.S.A.
>
>     On 9/13/12 3:10 AM, Pavan Kumar wrote:
>>
>>     Dear Jianwu,
>>
>>     I have installed Kepler on cluster.
>>     So I want to submit a workflow through PBS(Torque). Could you
>>     please let me know how can i achieve this.
>>
>>
>>
>>
>>     On Tue, Sep 11, 2012 at 10:29 PM, Jianwu Wang <jianwu at sdsc.edu
>>     <mailto:jianwu at sdsc.edu>> wrote:
>>
>>         Hi Pavan,
>>
>>             The simplest way to add tools in Kepler is configuring
>>         'External Execution' actor based on your tools. Connecting
>>         the tools are the same with connecting any other actors in
>>         Kepler.
>>
>>             We are currently working on a more advanced third-party
>>         tool addition and parallelization at BioKepler project
>>         (www.biokepler.org <http://www.biokepler.org>). The target of
>>         the project is to integrate popular existing bioinformatics
>>         tools and simplify users' own tool. We are still developing
>>         the bioKepler modules on top of Kepler to support it. You are
>>         welcome to check the website to follow our progress.
>>
>>         Best wishes
>>
>>         Sincerely yours
>>
>>         Jianwu Wang, Ph.D.
>>         jianwu at sdsc.edu <mailto:jianwu at sdsc.edu>
>>         http://users.sdsc.edu/~jianwu/ <http://users.sdsc.edu/%7Ejianwu/>
>>
>>         Assistant Project Scientist
>>         Scientific Workflow Automation Technologies (SWAT) Laboratory
>>         San Diego Supercomputer Center
>>         University of California, San Diego
>>         San Diego, CA, U.S.A.
>>
>>
>>         On 9/11/12 12:07 AM, Pavan Kumar wrote:
>>
>>             Dear Sir,
>>
>>             I am very new to Kepler. I have just installed Kepler on
>>             my Virtual Machine.
>>             I wanted to create my own workflow for NGS data analysis.
>>             Let me be clear, before creating a workflow, I have to
>>             integrarte tools in Kepler. Is that a right way.
>>             If so, Please let me know the steps in adding my own
>>             tools in Kepler and how to connect the toos inorder to
>>             create a workflow.
>>             Thanks in advance.
>>             Hope you will get back to me ASAP.
>>
>>
>>
>>             -- 
>>             Thanks & Regards,
>>             Pavan Kumar
>>             Project Engineer
>>             CDAC -KP
>>             Ph +91-7676367646 <tel:%2B91-7676367646>
>>
>>
>>
>>
>>
>>     -- 
>>     Thanks & Regards,
>>     Pavan Kumar
>>     Project Engineer
>>     CDAC -KP
>>     Ph +91-7676367646 <tel:%2B91-7676367646>
>
>
>
>
> -- 
> Thanks & Regards,
> Pavan Kumar
> Project Engineer
> CDAC -KP
> Ph +91-7676367646

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