Hi Gildas,

Thanks for the reply! Actually we are only using this as a local instance,
so there isn't any remote
server. :-)

Cheers,
Rui

On Mon, Oct 24, 2016 at 3:17 AM, Gildas Le Corguillé <
lecorgui...@sb-roscoff.fr> wrote:

> Hi
>
> Do you set some remote destination in the job_conf.xml like run the jobs
> on a HPC?
> If so, we have a similar issue and the solution was to let the upload1
> tool run on the local server not on the remote server.
>
> <tool id="upload1" destination="local"/>
>
> But maybe, it’s another problem :P
>
> Gildas
>
> -----------------------------------------------------------------
> Gildas Le Corguillé - Bioinformatician/Bioanalyste
>
> Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
> http://abims.sb-roscoff.fr
>
> Member of the Workflow4Metabolomics project
> http://workflow4metabolomics.org
>
> Station Biologique de Roscoff - UPMC/CNRS - FR2424
> Place Georges Teissier 29680 Roscoff FRANCE
> tel: +33 2 98 29 23 81
> ------------------------------------------------------------------
>
>
>
> Le 21 oct. 2016 à 20:58, Beginner TI <ruiwang...@gmail.com> a écrit :
>
> Hi,
>
> I'm trying to upload a file to a new galaxy instance for the first time,
> however an error happened, which never did in the past:
>
> Traceback (most recent call last):
>   File "/media/libraryfiles/galaxy/lib/galaxy/jobs/runners/__init__.py", line 
> 170, in prepare_job
>     job_wrapper.prepare()
>   File "/media/libraryfiles/galaxy/lib/galaxy/jobs/__init__.py", line 893, in 
> prepare
>     tool_evaluator.set_compute_environment( compute_environment, 
> get_special=get_special )
>   File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 63, 
> in set_compute_environment
>     visit_input_values( self.tool.inputs, incoming, validate_inputs )
>   File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", 
> line 92, in visit_input_values
>     visit_input_values( input.inputs, d, callback, new_name_prefix, 
> new_label_prefix, parent_prefix=new_name_prefix, **payload )
>   File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", 
> line 110, in visit_input_values
>     callback_helper( input, input_values, name_prefix, label_prefix, 
> parent_prefix=parent_prefix, context=context )
>   File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/__init__.py", 
> line 75, in callback_helper
>     new_value = callback( **args )
>   File "/media/libraryfiles/galaxy/lib/galaxy/tools/evaluation.py", line 62, 
> in validate_inputs
>     input.validate( value, request_context )
>   File "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/basic.py", 
> line 198, in validate
>     validator.validate( value, trans )
>   File 
> "/media/libraryfiles/galaxy/lib/galaxy/tools/parameters/validation.py", line 
> 99, in validate
>     raise ValueError( message )
> ValueError: You will need to reselect the file you specified 
> (/media/8tb/galaxy-data-store/database/tmp/upload_file_data_5wWKi5).
>
> It looks those files were successfuly uploaded, but the dataset files are
> all empty.
>
> Has anyone seen this?
>
> Thanks,
> Rui
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