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@kepler-project.org, where you will get more prompt and
comprehensive help.
Best wishes
Sincerely yours
Jianwu Wang, Ph.D.
jia...@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 <jia...@sdsc.edu
<mailto:jia...@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.
jia...@sdsc.edu <mailto:jia...@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 <jia...@sdsc.edu
<mailto:jia...@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.
jia...@sdsc.edu <mailto:jia...@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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