Hi Steve, try do like this example [1] [1] https://github.com/leobiscassi/autodock_vina_tools/blob/dev/tools/prepare_li... Cheers, On Fri, Oct 21, 2016 at 2:48 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
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Best regards, *Léo Biscassi*