Galaxy plug-in and configuration file

[squgusi]

Hi All

I created my galaxy instance and  added GenometriCorr, the page looks fine  however when I run the program galaxy gives me an error.
I know that galaxy per se is working well, I used it to produce the query and reference bed files.

My best guess is that there might be something wrong with the configuration file
I'm using the one provided in http://genometricorr.sourceforge.net/galaxy/example.ini

Does any one can help me with that?

thanks

[Alexander Favorov]

Thank you for your letter.

We'll try to understand what happens.

Please, can you describe the situation in more details (what error,
what was the sequence of galaxy commands, etc) and also can you please
share the bed files?

WBR, Sasha.

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[Cugusi, Simona]

Hi Sasha thanks for replying

my knowledge of programming is less than basics, so I apologize in advance if my explanation won't be too clear.

I'm working on a Mac 10.6, I'm in my galaxy instance and under "Mytools" I have the genometric corr software. When I open it I see what I'm supposed to: a tab to insert the configuration file, one for the query file, one for the reference file and one for the type of output. So far so good.
The bed files I'm using are those I'm sending you in this email, the configuration file is the sample file

http://genometricorr.sourceforge.net/galaxy/example.ini.

I tried to handle this file in several ways, copying and pasting and then changing the extension or just uploading it using the URL.


When I execute this is the error signal i get from galaxy:


Dataset generation errors

Dataset 34: Genometric Correlation on data 8, data 33, and data 13
The Galaxy framework encountered the following error while attempting to run the tool:

Traceback (most recent call last):
File "/Users/scugusi/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 94, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/Users/scugusi/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1009, in finish
self.sa_session.flush()
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/orm/scoping.py", line 114, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/orm/session.py", line 1718, in flush
self._flush(objects)
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/orm/session.py", line 1789, in _flush
flush_context.execute()
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/orm/unitofwork.py", line 331, in execute
rec.execute(self)
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/orm/unitofwork.py", line 475, in execute
uow
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/orm/persistence.py", line 59, in save_obj
mapper, table, update)
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements
execute(statement, params)
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/engine/base.py", line 1449, in execute
params)
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement
compiled_sql, distilled_params
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/engine/base.py", line 1698, in _execute_context
context)
File "build/bdist.macosx-10.6-intel/egg/sqlalchemy/engine/base.py", line 1691, in _execute_context
context)
File "build/bdist.macosx-10.6-intel/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 = ?' ('2013-06-27 18:12:30.751585', '', 'Error in library("GenometriCorr", warn.conflicts = F, verbose = F) : \n there is no package called \xe2\x80\x98GenometriCorr\xe2\x80\x99\nCalls: suppressPackageStartupMessages -> withCallingHandlers -> library\nExecution halted\n', 41)

Please let me know if you need more explanations i'll try to do my best.
thanks for helping me

________________________________________
From: genometri...@googlegroups.com [genometri...@googlegroups.com] on behalf of Alexander Favorov [fav...@sensi.org]
Sent: Thursday, June 27, 2013 1:56 PM
To: genometri...@googlegroups.com
Subject: Re: Galaxy plug-in and configuration file

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