Le 28.06.2010 16:03, David Withers a écrit :
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.
Thanks for these remarks David.
Indeed, I've tried on other accession, as Q9BZ11, and I successfully got
results. Even if with some other Swiss-Prot accession, I still not get
results, but I guess it is webservice related.
Thanks for all.
--
Raphaël Flores
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
taverna-users mailing list
[email protected]
[email protected]
Web site: http://www.taverna.org.uk
Mailing lists: http://www.taverna.org.uk/about/contact-us/
