Hi Can,

something went wrong with your join utility part of your Ubuntu
installation.

Can you translate that for us?

'join (GNU coreutils) 8.20\nCopyright (C) 2012 Free Software Foundation,
Inc.\nLisans GPLv3+: GNU GPL s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1
<http://gnu.org/licenses/gpl.html>.\nBu \xc3\x96zg\xc3\xbcr bir yaz\xc4
\xb1l\xc4\xb1md\xc4\xb1r: de\xc4\x9fi\xc5\x9ftirmek ve da\xc4\x9f\xc4
\xb1tmakta \xc3\xb6zg\xc3\xbcrs\xc3\xbcn\xc3\xbcz.\nYasalar\xc4\xb1n
izin verdi\xc4\x9fi \xc3\xb6l\xc3\xa7\xc3\xbcde, herhangi bir GARANT\xc4
\xb0 sunulmaz.\n\nMike Haertel taraf\xc4\xb1ndan yaz\xc4\xb1ld\xc4
\xb1.\n'

If the data is not confidential and small enough, maybe you can send it
me. Also please make sure that no unicode character are included in the
dataset or description.
I do not think an reinstallation will solve that problem.


Cheers,
Bjoern

> Hello everyone,
> 
> 
> Firstly, I am beginner. I am a new Galaxy user that installed the
> Galaxy locally into my ubuntu (13.04) installed computer. Everything
> is working perfectly right now. Galaxy is really awesome.
> 
> 
> To learn the basics, I started the basic tutorial (Galaxy101
> https://main.g2.bx.psu.edu/u/aun1/p/galaxy101) that helps too much.
> This tutorial consist a step for explaning "Compare Two Datasets"
> function. I did exactly everthing the instructor said however that
> module become red in History with following error:
> 
> 
> tool error
> An error occured with dataset: 
> Unable to finish job (screenshot of
> error: http://i.imgur.com/xHqhK72.png)
> 
> 
> I wrote the bug report at end of the mail.
> 
> 
> Interestingly, when I press "View" button, I get the data that I
> wanted. However, any metadata is seen. So I can not see the final
> results on the UCSC browser. I replicate the same module at public
> server, it didn't gave an error. 
> 
> 
> What might cause this kind of problem? Does reinstalling solve this
> problem? Would you please help me?
> 
> 
> Thank you everyone. 
> 
> 
> Traceback (most recent call last):
>   File "/home/can/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
> 94, in queue_job
>     job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/can/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1009,
> in finish
>     self.sa_session.flush()
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
>  line 114, in do
>     return getattr(self.registry(), name)(*args, **kwargs)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
>  line 1718, in flush
>     self._flush(objects)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
>  line 1789, in _flush
>     flush_context.execute()
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
>  line 331, in execute
>     rec.execute(self)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
>  line 475, in execute
>     uow
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
>  line 59, in save_obj
>     mapper, table, update)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
>  line 485, in _emit_update_statements
>     execute(statement, params)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1449, in execute
>     params)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1584, in _execute_clauseelement
>     compiled_sql, distilled_params
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1698, in _execute_context
>     context)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
>  line 1691, in _execute_context
>     context)
>   File
> "/home/can/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
>  line 331, in do_execute
>     cursor.execute(statement, parameters)
> ProgrammingError: (ProgrammingError) You must not use 8-bit
> bytestrings unless you use a text_factory that can interpret 8-bit
> bytestrings (like text_factory = str). It is highly recommended that
> you instead just switch your application to Unicode strings. u'UPDATE
> job SET update_time=?, stdout=?, stderr=? WHERE job.id
> = ?' ('2013-08-09 09:00:48.464260', 'join (GNU coreutils) 8.20
> \nCopyright (C) 2012 Free Software Foundation, Inc.\nLisans GPLv3+:
> GNU GPL s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1
> <http://gnu.org/licenses/gpl.html>.\nBu \xc3\x96zg\xc3\xbcr bir yaz
> \xc4\xb1l\xc4\xb1md\xc4\xb1r: de\xc4\x9fi\xc5\x9ftirmek ve da\xc4\x9f
> \xc4\xb1tmakta \xc3\xb6zg\xc3\xbcrs\xc3\xbcn\xc3\xbcz.\nYasalar\xc4
> \xb1n izin verdi\xc4\x9fi \xc3\xb6l\xc3\xa7\xc3\xbcde, herhangi bir
> GARANT\xc4\xb0 sunulmaz.\n\nMike Haertel taraf\xc4\xb1ndan yaz\xc4
> \xb1ld\xc4\xb1.\n', '', 41)
> 
> 
> 
> 
> Can Holyavkin
> 
> 
> PhD Student
> Istanbul Technical University
> Molecular Biology and Genetics Dept.
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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> 
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>   http://galaxyproject.org/search/mailinglists/


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