From: David W. <dav...@ma...> - 2010-06-28 14:03:30
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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 |