Hi Chadi

I am not familiar with the this tool

I recommend to try running the tool manually on the command line first, and then post the error on the mailing list (with a new subject) IF the error has something to do with Galaxy.

Hans-Rudolf

On 07/17/2013 05:00 PM, Chadi Abdul Kader El Farran wrote:

Dear Hans-Rudolf,

Thank you for your reply once again.

It appears that the problem is from a tool I installed in Galaxy. It is called ngsplot.

Whenever I try to do any analysis, I get the following error:

"Traceback (most recent call last): File "/home/swarna/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 94, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/swarna/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1009, in finish self.sa_session.flush() File "/home/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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/swarna/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 = ?' ('2013-07-17 14:56:30.112896', '\nzip error: Nothing to do! (data.zip)\n', 'mv: cannot stat \xe2\x80\x98data.zip\xe2\x80\x99: No such file or directory\n', 41) Tool execution generated the following error message: Unable to finish job"

Can you kindly help me?

With warmest regards,

Chadi EL Farran (Post Graduate Student) Dr. Jonathan Yuin-Han LOH's Laboratory #08-01, Institute of Molecular and Cell Biology (IMCB) 61 Biopolis Drive, Proteos Singapore 138673 Contact No: +65-91944793 E-mail: chadi@nus.edu.sg ________________________________________ From: Hans-Rudolf Hotz [hrh@fmi.ch] Sent: Wednesday, July 17, 2013 3:54 PM To: Chadi Abdul Kader El Farran Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Galaxy Local Admin user

Please keep all replies on the list by using "reply all" !

for my reply see below...

On 07/17/2013 06:58 AM, Chadi Abdul Kader El Farran wrote:

...

Dear Hans-Rudolf,

Thank you for your reply.

The problem was solved by restarting.

Now my problem is that I am unable to upload files into my Galaxy.

I have put the following code in Universe_wsgi.ini:

"# Directories of files contained in the following directory can be uploaded to a library from the Admin view library_import_dir = /upload"

However when I upload files to a data library, all files will seem to have no information (0 bytes)

That is very cryptic....and you need to provide more details

• did you get an error?
• how do you know the files are empty
• what happens if you work with the files

make sure to follow the wiki page:

http://wiki.galaxyproject.org/Admin/DataLibraries/Libraries

Hans-Rudolf

...

Can you kindly help me?

Thanks a lot for the support. With warmest regards

Chadi EL Farran (Post Graduate Student) Dr. Jonathan Yuin-Han LOH's Laboratory #08-01, Institute of Molecular and Cell Biology (IMCB) 61 Biopolis Drive, Proteos Singapore 138673 Contact No: +65-91944793 E-mail: chadi@nus.edu.sg ________________________________________ From: Hans-Rudolf Hotz [hrh@fmi.ch] Sent: Tuesday, July 16, 2013 9:39 PM To: Chadi Abdul Kader El Farran Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Galaxy Local Admin user

Hi

Just double checking: Have you restarted Galaxy?

Regards, Hans-Rudolf

On 07/16/2013 07:23 AM, Chadi Abdul Kader El Farran wrote:

...

Dear Madam/Sir,

I have installed Galaxy Local in our system. I registered as a user. However when I try to give admin status to some users, I am unable despite following the steps mentioned in the help.

"To give a user Galaxy admin privileges, add their Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini.

# this should be a comma-separated list of valid Galaxy users admin_users = user1@bx.psu.edu,user2@bx.psu.edu"

I have done what is mentioned above and the universe_wsgi.ini is edited accordingly. Still when I log on to Galaxy Local I don't see the admin tab.

Can you kindly help me.

With warmest regards

Chadi EL Farran (Post Graduate Student) Dr. Jonathan Yuin-Han Loh's Laboratory #08-01, Institute of Molecular and Cell Biology (IMCB) 61 Biopolis Drive, Proteos Singapore 138673 Contact No: +65-91944793 E-mail: chadi@nus.edu.sg ___________________________________________________________ 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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