I'm new to linux so my question might need a really simple answer.
I'm trying to use "RepliconWrench" (https://github.com/RepliconBioinfo/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?
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.
Please follow-up to let us know how you made out. For good karma, mark a reply as the answer if it helped!