Problem to upload data to Galaxy when using pbed file format
Dear all, I am trying to upload data from PLINK (.bed, .bim and .fam-files) for the pbed file format using a local installation of Galaxy but it is not working. The local Galaxy installation was done yesterday, following the instructions at: https://wiki.galaxyproject.org/Admin/GetGalaxy First, I click on the Get Data tool, I then select pbed as "File Format", the page reloads and I now can enter the three files (.bed, .bim, .fam). Once I click "Execute" the job starts but never seems to finish. If I look in the log output from Galaxy I get the following error: galaxy.tools ERROR 2014-11-13 13:24:52,226 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 2180, in handle_single_execution job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 2738, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload.py", line 21, in execute uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs, history=history ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload_common.py", line 246, in get_uploaded_datasets data.uuid = uploaded_dataset.uuid AttributeError: 'Bunch' object has no attribute 'uuid' Any idea what could be the problem? Kind regards, Johan
Hello Johan, Thanks for the bug report. I can confirm this problem - I have opened up a pull request with the fix to galaxy-central's stable branch (https://bitbucket.org/galaxy/galaxy-central/pull-request/567/stable-bugfix-c...). -John On Thu, Nov 13, 2014 at 8:29 AM, <tjkarlsson@uma.es> wrote:
Dear all,
I am trying to upload data from PLINK (.bed, .bim and .fam-files) for the pbed file format using a local installation of Galaxy but it is not working.
The local Galaxy installation was done yesterday, following the instructions at: https://wiki.galaxyproject.org/Admin/GetGalaxy
First, I click on the Get Data tool, I then select pbed as "File Format", the page reloads and I now can enter the three files (.bed, .bim, .fam).
Once I click "Execute" the job starts but never seems to finish. If I look in the log output from Galaxy I get the following error:
galaxy.tools ERROR 2014-11-13 13:24:52,226 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 2180, in handle_single_execution job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/__init__.py", line 2738, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload.py", line 21, in execute uploaded_datasets = upload_common.get_uploaded_datasets( trans, '', incoming, precreated_datasets, dataset_upload_inputs, history=history ) File "/home/mrsbm/galaxy/galaxy2/galaxy-dist/lib/galaxy/tools/actions/upload_common.py", line 246, in get_uploaded_datasets data.uuid = uploaded_dataset.uuid AttributeError: 'Bunch' object has no attribute 'uuid'
Any idea what could be the problem?
Kind regards, Johan ___________________________________________________________ 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: http://lists.bx.psu.edu/
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John Chilton -
tjkarlsson＠uma.es