Running My Own Walker On Gatk

Question

[Pascal]

Hi.

I can't get my GATK walker encountered by GATK framework altough I have the compiled class under the CLASSPATH umbrella:

pmaugeri@ubuntu-bio:~/gatk$ ls $CLASSPATH
FirstWalker.class  HelloWalker.class  HelloWorld.class
pmaugeri@ubuntu-bio:~/gatk$ java -jar GenomeAnalysisTK-1.2-60-g585a45b/GenomeAnalysisTK.jar -T HelloWalker
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.2-60-g585a45b): 
[...]
##### ERROR MESSAGE: Could not find walker with name: HelloWalker
##### ERROR ------------------------------------------------------------------------------------------

Is there something else to do to define my walker than what is described in Your first walker ?

I noticed for instance that CountReadsWalker is called with -T CountReads but the corresponding class is CountReadsWalker. I suspect there is a declaration or mapping to be done.

Thanks in advance for your help.

[Russh]

does Hello appear amongst the walker list when you run 'java -jar GenomeAnalysisTK.jar' without any other arguments

Answer 1

[Pierre Lindenbaum]

you have to put the compiled walker in the classpath. So the right command would be to call:

java -cp GenomeAnalysisTK-1.2-60-g585a45b/GenomeAnalysisTK.jar:.  org.broadinstitute.sting.gatk.CommandLineGATK -T HelloWalker

[Pascal]

Many thanks Pierre for your help !

Although I finally have to use "-T Hello" and not "-T HelloWalker" as stated by russH.

Answer 2

[Russh]

you are correct on the last point: you should use '... -T Hello '

[Pascal]

Sorry, I forgot to add that I actually tried with -T Hello too and it didn't help. Thanks for your fast answer anyway. This must be something obvious that I forgot :-))

[Russh]

haha, whoever voted this up is being wayy too kind

[Pascal]

I voted you up too because at the end I had to use "-T Hello" so your contribution is helpful too ;-) Thanks.