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 ${signal}.wav &amp;
        /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$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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