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.