Using a soft link for this is a common pattern, and should be followed with && (ideally using XML CDATA to avoid escaping everything like & etc), and quote the filenames just in case there are any spaces. e.g. https://github.com/galaxyproject/tools-iuc/blob/master/tools/trinity/run_de_... For reference, in tools-iuc there are over 400 soft link examples: $ grep "ln -s" tools/*/*.xml | wc -l 446 Peter On Fri, Oct 21, 2016 at 5:48 PM, Steve Cassidy <steve.cassidy@mq.edu.au> wrote:
Hi, I’m wrapping a tool that needs it’s input to have a known file extension (an audio file, eg. .wav). Since Galaxy stores all data as .dat files the tool is falling over since it doesn’t know what .dat is.
I thought I’d be able to get around this by hard linking the .dat file to the same name with a .wav extension (dataset_1.dat.wav), this works when I try it with the tool on the command line but within Galaxy it fails, here’s my <command>:
ln $signal ${signal}.wav & /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language BPF=$bpf INSKANTEXTGRID=$inskantextgrid INSORTTEXTGRID=$insorttextgrid MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen WEIGHT=$weight INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence OUTSYMBOL=$outsymbol OUT=$output SIGNAL=${signal}.wav
resulting in the job command line:
ln /tmp/tmp7AZvx7/files/000/dataset_2.dat /tmp/tmp7AZvx7/files/000/dataset_2.dat.wav & /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=aus BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10 MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0 NOINITIALFINALSILENCE=no OUTSYMBOL=sampa OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat SIGNAL=/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav
I’m getting an error message from the tool:
sox FAIL formats: can't open input file `/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found
this suggests that the hard link didn’t get made. I tried copying the file instead but got the same result.
I could go in and patch the tool script to be more forgiving but it would be good to find a solution that didn’t require that if possible.
Any pointers appreciated.
Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy
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