Dear Alan, On 10/11/2012 12:56 PM, Alan R Williams wrote: > On 11/10/2012 10:58, Bas Jansen wrote: >> Dear All, > Hello > >> I have a question regarding using a program that i wrote inside a tool >> service of taverna, i am using string replacement to take the input >> parameters and the echo of the command gives the proper syntax (so that >> i can run the command on the bash and it does what i want) but running >> it inside taverna returns an error message from the program that i wrote >> (that it doesn't get a correct input file). >> >> Would anyone have any clues or ideas what might be causing this? > What does PeptMoiety expect as its -f and -m parameters? Does it expect > a filepath or a string? > > I think the problem may be that you are passing input and mgf as string > parameters. You may want them to be file inputs. You would then change > the command to be > > /data/programming/C/PeptMoiety2/PeptMoiety -f input -m mgf > > You will probably then have problems because the file called input > contains a list of other files. Taverna will not know that those files > are needed by PeptMoiety and so would not copy them into the service > call's working directory. However, there are ways round this, but first > check what PeptMoiety wants. PeptMoiety expects two files passed to it (when running it on the command line), I would like to try the file option but will need the way to go around this issue with input being a list of files so if you would be willing to share that, that would be greatly appreciated. >> I included the executable, workflow and 2 files that can be used as >> input, if the command is executed it should give a segmentation fault >> because the 'actual' data is not included. >> >> Cheers, >> >> Bas Jansen MSc, >> Leiden University Medical Center > Alan > Bas
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