Replicon - unable to use


I’m new to linux so my question might need a really simple answer.

I’m trying to use “RepliconWrench” (, and I want to use the “BedToILPS” script.

the example says that the code to run is something like this: “java -jar RepliconWrench.jar BedToIPLS -i refSeq.bed -o refSeqIPLS”. when I try to use it, I get “Unable to access jarfile RepliconWrench.jar”.

How can I run this?

Thank you,


The likeliest problem is you are not executing your command in the directory which contains the .jar file. I confirmed the .jar file works, at least on Windows.

On unix, files are case sensitive:

java -jar RepliconWrench.jar

Or there is some sort of permissions issue; try copying the .jar file to a different directory, and execute your command there.

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