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
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