On Aug 31, 2012, at 8:33 AM, Geert Vandeweyer wrote:

> 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

Although it should generate an error rather than an empty file, can you ensure 
that new_file_path in Galaxy's config is pointed at a filesystem that is shared 
between the cluster and the Galaxy server?  If it is, you may need to add some 
debugging to the upload tool to figure out exactly where the problem is.

--nate

> 
> 
> 
> 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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