Hi Nate,

The datafile is really empty on the disk (size 0, checked at the "full path" etnry from the dataset info).


Best regards,

Geert Vandeweyer



On 08/29/2012 06:05 PM, Nate Coraor wrote:
On Jul 16, 2012, at 6:14 AM, Geert Vandeweyer wrote:

Hi,

We have set up a local instance of galaxy-dist, using pbs-python to communicate 
with our HPC. Everything is working great, except for the upload functionality.

When I assign the upload1 to local:/// , uploading of small files through the 
web-site works, and upload of large files by ftp works as well. When I let 
upload1 to be handled by the default_cluster_job_runner ( = pbs:///), I get 
empty data sets. Galaxy does not report any errors however and the data state 
is ok.

Has anybody seen this issue and solved it? Using the local:/// job handler 
causes a massive performance hit on the galaxy process.

Best regards,

Geert Vandeweyer
Hi Geert,

Sorry for the delayed response.  If you're still having this issue, if you view 
the empty dataset, can you see the data it's supposed to contain?  i.e. does 
the underlying output file for the upload tool actually contain the data, or is 
it really empty on disk?

--nate

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--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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