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_analysis.xml#L16 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.cass...@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/ ___________________________________________________________ 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/
