On Fri, Jun 8, 2012 at 9:15 AM, Nicholas Robinson <nicholas.robin...@nofima.no> wrote: > Hi, > > 1. INPUT > I am trying to make a simple tool that sends a command to run crimap without > a wrapper ie. > ............. > <command> > crimap $param_file $option >$output1 > </command> > .............. > > However, crimap expects a .par file as input (ie. $param_file should be a > .par file). Because of this I get the error: > ERROR: Parameter file > '/home/galaxy/galaxy-dist/database/job_working_directory/001/1434/tmpe5hErw' > does not have '.par' suffix > > ... > > Is there a simple way around this (using more lines in the command)?
You could try something like this (untested): <command> ln -s $param_file $param_file.par; crimap $param_file $option >$output1 </command> The idea here is to tell Galaxy to issue two commands, the first a shell call to create a symlink with the desired extension pointing at the input filename from Galaxy. i.e. If $param_file was /path/to/file/dataset_123.dat you'd make a symlink /path/to/file/dataset_123.dat.par - but check if you need to remove the symlink afterwards. Anything more that that and I would use a wrapper script in whatever you are most comfortable with (e.g. shell, Perl, or Python). e.g. <command> my_script $param_file $option $output1 </command> where the my_script file is marked executable with a hashbang (or set the interpreter in the command tag), and the script could be just: #/bin/bash ln -s $param_file $param_file.par crimap $param_file $option > $output1 rm $param_file.par Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
