Great job Dan! It works! Thank you a lot again! The revision 29738 is ok. I have some R warnings and with Ptolemy at revision 63376 I still have some troubles with ant force-ptolemy compile but the generation of the PDF is doing it as well.
If I have new suggestions or problems I'll notice them. Thanks! Albert 2012/4/17 Daniel Crawl <[email protected]> > > I fixed the problem and you can now specify parameters when > executing KAR workflows: > > kepler -runkar -nogui [-param1 value1 ...] workflow.kar > > --dan > > > > On 4/17/12 5:57 AM, Josep Maria Campanera Alsina wrote: > >> Dear All, >> This is Josep M. Campanera who has been using kepler for >> bioinformatics. Now I'm developing with Albert Vilà (and others) a web >> front-end for kepler that we will make available once the first tests >> are satisfactory. Additionally we are also developing a perl actor for >> kepler. >> >> As mentioned by Albert, It is crucial the command line execution with >> parameters of kar files for continuing our project. Dan says that >> there is a bug which impedes the execution of kar files by means of >> command line execution with parameters. In line with Dan's comments, >> we would like to know aproximately when this bug is going to be >> fixed. >> >> 1) Are you thinking of days, weeks or months? >> >> 2) In case we need to wait for a long period, which is the best >> strategy to surpass that drawback meanwhile? >> >> Thank you very much, >> >> Josep M. Campanera, >> >> >> Hi Albert, >> >> I'll look into fixing this. It would be nice to have a consistent set of >> command-line options for executing momls and kars. >> >> --dan >> >> >> On 4/16/12 3:00 AM, Albert Vilà Picas wrote: >> >> Hi all, >> >> I have read in other e-mails that now is not possible to execute .kar >> workflows with parameters? >> We run a command line KAR with reporting layout added running -runwf >> -nogui >> [-param value]*. >> I have tried also with -runkar and I have the same error. >> Is that a Ptolemy error that is not suitable? We're doing a great >> project >> with Kepler >> and is necessary to run command line kar wf changing the value of the >> input >> parameters. >> >> Here is the stack trace: >> >> [null] common tabpane configuration overridden by reporting >> [null] Ran additional initialization for module reporting from >> class >> org.kepler.module.reporting.**Initialize >> [null] loading: org.kepler.**KeplerConfigurationApplication >> args: >> ptolemy/configs/kepler/**ConfigNoGUIWithCache.xml -runThenExit >> -epochs 100 >> /home/sbi/sbi-services/sbi-**home/Temporal/MLRAlbert.kar >> [null] invoking: org.kepler.**KeplerConfigurationApplication** >> .main >> [null] Kepler Initializing... >> [null] Unsupported file type or connection not available: >> file:/home/sbi/sbi-services/**sbi-home/Temporal/MLRAlbert.**kar >> [null] Command failed >> [null] java.lang.Exception: Failed to parse >> "ptolemy/configs/kepler/**ConfigNoGUIWithCache.xml -runThenExit >> -epochs 100 >> /home/sbi/sbi-services/sbi-**home/Temporal/MLRAlbert.kar" >> [null] at >> ptolemy.actor.gui.**ConfigurationApplication.**throwArgsException(** >> ConfigurationApplication.java:**791) >> [null] at >> org.kepler.**KeplerConfigurationApplication**.<init>(** >> KeplerConfigurationApplication**.java:339) >> [null] at >> org.kepler.**KeplerConfigurationApplication**.main(** >> KeplerConfigurationApplication**.java:639) >> [null] at sun.reflect.**NativeMethodAccessorImpl.**invoke0(Native >> Method) >> [null] at >> sun.reflect.**NativeMethodAccessorImpl.**invoke(** >> NativeMethodAccessorImpl.java:**57) >> [null] at >> sun.reflect.**DelegatingMethodAccessorImpl.**invoke(** >> DelegatingMethodAccessorImpl.**java:43) >> [null] at java.lang.reflect.Method.**invoke(Method.java:616) >> [null] at org.kepler.Kepler.load(Kepler.**java:445) >> ... >> >> Note that with the same workflow.kar without parameters runs perfectly >> keeping the results and generating the .PDF from reporting. >> We need that the workflow must be a .kar and not an .xml >> >> Thank you very much >> >> --Albert >> ______________________________**_________________ >> Kepler-users mailing list >> Kepler-users@kepler-project.**org <[email protected]> >> http://lists.nceas.ucsb.edu/**kepler/mailman/listinfo/**kepler-users<http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users> >> > >
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