7:54 a.m.
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(a)nus.edu.sg
________________________________________
From: Hans-Rudolf Hotz [hrh(a)fmi.ch]
Sent: Tuesday, July 16, 2013 9:39 PM
To: Chadi Abdul Kader El Farran
Cc: galaxy-dev(a)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(a)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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
3 p.m.
New subject: Galaxy Local Admin user
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(a)nus.edu.sg
________________________________________
From: Hans-Rudolf Hotz [hrh(a)fmi.ch]
Sent: Wednesday, July 17, 2013 3:54 PM
To: Chadi Abdul Kader El Farran
Cc: galaxy-dev(a)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(a)nus.edu.sg
________________________________________
From: Hans-Rudolf Hotz [hrh(a)fmi.ch]
Sent: Tuesday, July 16, 2013 9:39 PM
To: Chadi Abdul Kader El Farran
Cc: galaxy-dev(a)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(a)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/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
3:45 p.m.
New subject: Galaxy Local Admin user
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(a)nus.edu.sg
________________________________________
From: Hans-Rudolf Hotz [hrh(a)fmi.ch]
Sent: Wednesday, July 17, 2013 3:54 PM
To: Chadi Abdul Kader El Farran
Cc: galaxy-dev(a)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(a)nus.edu.sg
> ________________________________________
> From: Hans-Rudolf Hotz [hrh(a)fmi.ch]
> Sent: Tuesday, July 16, 2013 9:39 PM
> To: Chadi Abdul Kader El Farran
> Cc: galaxy-dev(a)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(a)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/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>>
>
3484
days inactive
3484
days old
galaxy-dev@lists.galaxyproject.org
2 comments
2 participants
participants (2)
-
Chadi Abdul Kader El Farran -
Hans-Rudolf Hotz