On 28/06/2010 14:13, Raphaël Flores wrote:
> Hello all,
>
> I've tried to use attached worklow (which gets fasta sequence from
> Swissprot related to an accession number) with bootstrapper
> (./executeworkflow.sh, which calls ./taverna-bootstrap-1.7.2.1.jar)
> but instead of creating 2 result files ("fastaSequence" and
> "output"), it has created 2 folders/directories with these names, but
> without any content.
>
> Here is the command line I use :
>
> ../executeworkflow.sh -input SwissProtAcc
> protic_accession_5004616955195094923.txt
> file:getFastaSeqFromSwissProtAcc.xml -output ./result
>
> Files are in attachment. For information:
>
> $ ls -lFh result/ total 8,0K drwxr-xr-x 2 rflores rflores 4,0K
> 2010-06-28 15:03 fastaSequence/ -rw-r--r-- 1 rflores rflores 2,3K
> 2010-06-28 15:03 progressReport.xml
>
> $ java -version java version "1.6.0_0" OpenJDK Runtime Environment
> (build 1.6.0_0-b11) OpenJDK Client VM (build 1.6.0_0-b11, mixed mode,
> sharing)I get this behavour only with this workflow. Any idea why ?
> And how make the workflow outputs being text files rather than
> folders ?
>
> Any help would be greatly appreciated.
>
> Raphaël.
Hi Raphaël,
I tried running your workflow in the Taverna 1.7.2.1 workbench and the
results I get are two empty lists. When run from the command line you
will get a directory per output which contains a file for each element
of the result list. As the results are empty lists, you will get empty
directories.
David.
--
David Withers
School of Computer Science, University of Manchester,
Oxford Road, Manchester, M13 9PL, UK.
+44 (0)161 275 0683
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