Question

I ran a perl script in biotoolbox package.(http://code.google.com/p/biotoolbox/)
but got the error message related with jarfile.

$./bar2wig.pl

 This program will convert bar files to a wig file
 Usage:
 bar2wig.pl [--options...] <filename>

  Options:
  --in <filename> or <directory>
  --out <filename> 

$  ./bar2wig.pl --in  /Users/biotoolbox/scripts/ --out example

This program will convert bar files to a wig file
checking input file(s)....
converting to gr files...
Unable to access jarfile /usr/local/USeq/Apps/Bar2Gr
writing wig file...
cleaning up temp files... done

i am not sure what to do for the error: unable to access jarfile .
it looks like java related error, although this script is perl.

any comments for this?

Answer 1

Yes, obviously it couldn’t find the jarfile. Read the Wiki entry on jar, but suffice to say it’s just a portable package of java files.

You’re going to need to download that jar file and define where it’s located within the configuration file biotoolbox.cfg