Dears,
Regarding to R shell iissues I would like to ask something: I want to run an
R script using T2server which generates a png plot as output. I am able to
retrieve a single plot if I run the Rscript once. However if I want to loop
through a data-file (example: for every ID in the data, run some R code),
the system is not able to generate different plots and save in differents
names, since it must be output as a variable png(variable) --> outputport
variable.
If I create a iteration counter and I loop inside Rscript, (let's say from 1
to 10), my final workflow outputs are the iteration 10 and the output of the
10th ID number, so it seems to be overwriting the files.
Is there a clear solution for this looping issue. I tried to loop in the PHP
that calls the server, but this is not so clean and generates tomcat
saturation.
Thanks,
Regards,
Albert Mascarell Creus
www.o2hlink.com
2010/11/24 Alexandra Nenadic <[email protected]>
> Hello Marco,
>
> Indeed the current documentation on Rshell/RServer refers to Taverna 1:
>
> http://www.mygrid.org.uk/usermanual1.7/rshell_processor.html#rshell_using
>
> We will try to update this documentation for Taverna 2 by the end of the
> week and include it as part of the Taverna 2 User Manual (currently in
> preparation). However, you can still use the Taverna 1 documentation as the
> UI differences between Taverna 1 and 2 regarding R services are not that
> big.
>
> R workflows that worked in Taverna 1 should also work in Taverna 2. Note
> that it is a bit difficult to provide workflows with R services that work
> universally as they also require an R Serve running, which we do not provide
> (normally users have an R server running locally).
>
> Regards,
> Alex
>
>
> On 24/11/2010 10:24, Marco Roos wrote:
>
> Dear Taverna user / developer,
>
> We are working on a gene expression analysis workflow (Taverna 2) in which
> we wish to include various R scripts. There is now a lot of useful
> documentation on the Taverna web site, but not so much on using Rshell in
> Taverna 2.
>
> Our first question is if there is perhaps more documentation that we
> overlooked, or if more documentation on Rshell is coming.
>
> Our second question is if you have examples of workflows that help explain
> how Rshell can be used in Taverna2. Tutorial-level workflows would be best.
> Most examples that we find on myExperiment are for Taverna 1.
>
> Many thanks,
> Dennis and Marco
>
>
> --
> Marco Roos (PhD) <http://home.medewerker.uva.nl/m.roos1>
> *BioSemantics group* <http://www.biosemantics.nl>, Human Genetics
> department <http://www.humgen.nl>, Leiden University Medical
> Centre<http://www.lumc.nl>
> Albinusdreef 2 (Building 2, room S3-46)
> 2333 ZA Leiden
> Tel. +31 (0) 71 526 8642
> *Adaptive Information Disclosure group* <http://adaptivedisclosure.org/>,
> Informatics
> Institute <http://www.science.uva.nl/ii>, University of
> Amsterdam<http://www.uva.nl/>
> Kruislaan 403 ( room
> N2.30<http://remote.science.uva.nl/%7Eroos/Kruislaan403_N230.png>)
> 1098 SJ Amsterdam
> Tel. +31 (0) 20 525 7522
> *Communities:*
> Professional: LinkedIn <http://www.linkedin.com/in/marcoroos>,
> myExperiment <http://www.myexperiment.org/users/18> Personal:
> Hyves<http://mroos62.hyves.nl/>
>
>
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