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 < lecorguille@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.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 ___________________________________________________________ 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/
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