Am 26.11.2013 11:17, schrieb Alan R Williams:
First of all, thanks for the fast response to my question.
I would try the tool service rather than the beanshell. So create a tool
service where the command is
java -Xms256m -Xmx512m -jar /path/to/Programm.jar %%input1%% %%input2%%
%%input3%% %%output%%
and have three input ports and one output.
Also, how are you passing around the data? Once it gets large then it is
better to pass it as files rather than data. So (assuming input1 is the
large file), have a command that says
java -Xms256m -Xmx512m -jar /path/to/Programm.jar input1 %%input2%%
%%input3%% %%output%%
I'm trying to use the tool service now, but I'm not able to parse the
input files correctly.
java -Xms256m -Xmx4g -jar GenomeAnalysisTK-2.7-4/GenomeAnalysisTK.jar -T
UnifiedGenotyper -R refFile -I bamFile -glm BOTH -L regionFile --dbsnp
dbsnpFile -o variantFile -dcov 200 -stand_emit_conf 10 -stand_call_conf 30
The input files are refFile, bamFile, regionFile and dbsnpFile. I
configured them as file inputs in the tool options.
Is there anything wrong with my syntax ? In which way Taverna executes
this command line? What are the differences to an execution on
gnome-terminal?
I'm really thankful for your help
Best,
Julian
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