starting run_reports.sh fails

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starting run_reports.sh fails

Joachim Jacob
run_reports.sh dies silently.

Its last will in reports_webapp.log states:

Traceback (most recent call last):
   File "./scripts/paster.py", line 33, in <module>
     serve.run()
   File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 1056, in run
     invoke(command, command_name, options, args[1:])
   File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 1062, in invoke
     exit_code = runner.run(args)
   File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 227, in run
     result = self.command()
   File "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
line 650, in command
     app = loadapp( app_spec, name=app_name, relative_to=base,
global_conf=vars)
   File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
350, in loadapp
     return loadobj(APP, uri, name=name, **kw)
   File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
375, in loadobj
     return context.create()
   File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
813, in create
     return self.object_type.invoke(self)
   File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
249, in invoke
     return fix_call(context.object, context.global_conf,
**context.local_conf)
   File
"/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line
97, in fix_call
     val = callable(*args, **kw)
   File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", line
61, in app_factory
     add_ui_controllers( webapp, app )
   File
"/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py", line
33, in add_ui_controllers
     from galaxy.web.base.controller import BaseUIController
   File "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py",
line 23, in <module>
     from galaxy.visualization.genome.visual_analytics import get_tool_def
   File
"/home/galaxy/galaxy-dist/lib/galaxy/visualization/genome/visual_analytics.py",
line 3, in <module>
     from galaxy.tools.parameters.basic import IntegerToolParameter,
FloatToolParameter, SelectToolParameter
   File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
57, in <module>
     from galaxy.visualization.genome.visual_analytics import
TracksterConfig
ImportError: cannot import name TracksterConfig

Anybody knowing the recipe to reanimate the patient? Thanks.
BTW, this is the first time I am starting up run_reports.sh after the 1
april/8 april update. Did not had this issue before.


Joachim

--
Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: starting run_reports.sh fails

Joachim Jacob
Already reported in Trello
https://trello.com/c/o0S3klAF

Thanks for the fix!

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/15/2013 03:19 PM, Joachim Jacob | VIB | wrote:

> run_reports.sh dies silently.
>
> Its last will in reports_webapp.log states:
>
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 33, in <module>
>     serve.run()
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
> 1056, in run
>     invoke(command, command_name, options, args[1:])
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
> 1062, in invoke
>     exit_code = runner.run(args)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
> 227, in run
>     result = self.command()
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line
> 650, in command
>     app = loadapp( app_spec, name=app_name, relative_to=base,
> global_conf=vars)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 350, in loadapp
>     return loadobj(APP, uri, name=name, **kw)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 375, in loadobj
>     return context.create()
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 813, in create
>     return self.object_type.invoke(self)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 249, in invoke
>     return fix_call(context.object, context.global_conf,
> **context.local_conf)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
> line 97, in fix_call
>     val = callable(*args, **kw)
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py",
> line 61, in app_factory
>     add_ui_controllers( webapp, app )
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py",
> line 33, in add_ui_controllers
>     from galaxy.web.base.controller import BaseUIController
>   File "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py",
> line 23, in <module>
>     from galaxy.visualization.genome.visual_analytics import get_tool_def
>   File
> "/home/galaxy/galaxy-dist/lib/galaxy/visualization/genome/visual_analytics.py",
> line 3, in <module>
>     from galaxy.tools.parameters.basic import IntegerToolParameter,
> FloatToolParameter, SelectToolParameter
>   File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
> 57, in <module>
>     from galaxy.visualization.genome.visual_analytics import
> TracksterConfig
> ImportError: cannot import name TracksterConfig
>
> Anybody knowing the recipe to reanimate the patient? Thanks.
> BTW, this is the first time I am starting up run_reports.sh after the
> 1 april/8 april update. Did not had this issue before.
>
>
> Joachim
>

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: starting run_reports.sh fails

Joachim Jacob
No prob. Actually, I have found the answer thanks to the GalaxyAdmins
meeting yesterday, where somebody extensively pointed to Trello ;-)

Cheers
J

Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 05/15/2013 07:00 PM, Dannon Baker wrote:

> Heh, thanks for answering both halves of the email before I could even
> get to it :)
>
>
> On Wed, May 15, 2013 at 12:03 PM, Joachim Jacob | VIB |
> <[hidden email] <mailto:[hidden email]>> wrote:
>
>     Already reported in Trello
>     https://trello.com/c/o0S3klAF
>
>     Thanks for the fix!
>
>
>     Joachim Jacob
>
>     Rijvisschestraat 120, 9052 Zwijnaarde
>     Tel: +32 9 244.66.34 <tel:%2B32%209%20244.66.34>
>     Bioinformatics Training and Services (BITS)
>     http://www.bits.vib.be
>     @bitsatvib
>
>     On 05/15/2013 03:19 PM, Joachim Jacob | VIB | wrote:
>
>         run_reports.sh dies silently.
>
>         Its last will in reports_webapp.log states:
>
>         Traceback (most recent call last):
>           File "./scripts/paster.py", line 33, in <module>
>             serve.run()
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
>         line 1056, in run
>             invoke(command, command_name, options, args[1:])
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
>         line 1062, in invoke
>             exit_code = runner.run(args)
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
>         line 227, in run
>             result = self.command()
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py",
>         line 650, in command
>             app = loadapp( app_spec, name=app_name, relative_to=base,
>         global_conf=vars)
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>         line 350, in loadapp
>             return loadobj(APP, uri, name=name, **kw)
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>         line 375, in loadobj
>             return context.create()
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>         line 813, in create
>             return self.object_type.invoke(self)
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>         line 249, in invoke
>             return fix_call(context.object, context.global_conf,
>         **context.local_conf)
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py",
>         line 97, in fix_call
>             val = callable(*args, **kw)
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py",
>         line 61, in app_factory
>             add_ui_controllers( webapp, app )
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/webapps/reports/buildapp.py",
>         line 33, in add_ui_controllers
>             from galaxy.web.base.controller import BaseUIController
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py",
>         line 23, in <module>
>             from galaxy.visualization.genome.visual_analytics import
>         get_tool_def
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/visualization/genome/visual_analytics.py",
>         line 3, in <module>
>             from galaxy.tools.parameters.basic import
>         IntegerToolParameter, FloatToolParameter, SelectToolParameter
>           File
>         "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
>         57, in <module>
>             from galaxy.visualization.genome.visual_analytics import
>         TracksterConfig
>         ImportError: cannot import name TracksterConfig
>
>         Anybody knowing the recipe to reanimate the patient? Thanks.
>         BTW, this is the first time I am starting up run_reports.sh
>         after the 1 april/8 april update. Did not had this issue before.
>
>
>         Joachim
>
>
>     ___________________________________________________________
>     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/
>
>

___________________________________________________________
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/