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 <http://abims.sb-roscoff.fr/> Member of the Workflow4Metabolomics project http://workflow4metabolomics.org <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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
