Dear Developers

I'm currently looking at develop a tool for a local pipeline, and want to make symlinks as part of the script in the "command" section of the tool XML - something like e.g.

  <command interpreter="bash"><![CDATA[
  ## Create links to input FASTQs and Final_names.txt file
  #for $fq_pair in $fastq_pairs
    ln -s "${fq_pair.fastq_r1}" &&
  #end for

But when I try running the tool I get a failure with the message:

Fatal error: Exit code 127 ()
bash: /PATH/TO/TOOL/DIR/ln: No such file or directory

(NB I've snipped out the real path above, but essentially it's the directory where the tool XML is installed.)

I know that it's permissible to use 'cp' and 'mv' in this context, so is 'ln' treated differently? Is there an alternative way to make symlinks in the command?

Thanks for your help!

Best wishes


Peter Briggs
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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