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

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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
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Le 21 oct. 2016 à 20:58, Beginner TI <ruiwang.sz@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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