universe_wsgi.ini question for Cistrome

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

universe_wsgi.ini question for Cistrome

Rui Wang
Hi Guys,

Are there anyone who is using Cistrome?

I tried to merge Cistrome's setting into our own galaxy instance. A new entry is

# Path to the static library files for assembly, ceaslib, chromLen, conservation, liftOver and MAT-lib
# Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path'
# default would be in tool-data/ folder
cistrome_static_library_path = /home/bioinfoadmin/app/cistrome-apps/cistrome_library

However, I got error when I tried CEAS: Enrichment on chromosome and annotation:

 

*****************************************************************************

Dataset 23: CEAS: Enrichment on chromosome and annotation on data 16 and data 13

The Galaxy framework encountered the following error while attempting to run the tool:

 

Traceback (most recent call last):

  File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 121, in prepare_job

    job_wrapper.prepare()

  File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/jobs/__init__.py", line 707, in prepare

    config_filenames = self.tool.build_config_files( param_dict, self.working_directory )

  File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 2609, in build_config_files

    f.write( fill_template( template_text, context=param_dict ) )

  File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template

    return str( Template( source=template_text, searchList=[context] ) )

  File "/home/bioinfoadmin/app/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__

    return getattr(self, mainMethName)()

  File "cheetah_DynamicallyCompiledCheetahTemplate_1391037616_15_43258.py", line 274, in respond

NotFound: cannot find 'cistrome_static_library_path' while searching for '__app__.config.cistrome_static_library_path'

 

Tool execution generated the following error message:

 

failure preparing job

 

********************************************************************************


I'm quite confused since '__app__.config.cistrome_static_library_path' should be defined? or right now __app__ is dropped

as Galaxy evolves? Besides, what does the comment mean by


# Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path'

Does that mean that we should not be using __app__.config...but how to use this? I tried to insert 

'from galaxy import config' 

into the xml file but only got error...

I'll appreciate any input.

Thanks,
Rui



___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: universe_wsgi.ini question for Cistrome

Ido Tamir
I have CEAS as a tool. I wrapped the standalone CEAS version. I tried adding a binary datatype for the annotation db but even with the binary datatype upload somehow did not work (IIRC galaxy tried to convert it to ascii).
I then put the database as a selectable parameter in a dropdown list, because users anyway would not create and upload their own annotation db.

best,
ido

On Feb 27, 2014, at 7:13 AM, ruiwang.sz <[hidden email]> wrote:

> Hi Guys,
>
> Are there anyone who is using Cistrome?
>
> I tried to merge Cistrome's setting into our own galaxy instance. A new entry is
>
> # Path to the static library files for assembly, ceaslib, chromLen, conservation, liftOver and MAT-lib
> # Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path'
> # default would be in tool-data/ folder
> cistrome_static_library_path = /home/bioinfoadmin/app/cistrome-apps/cistrome_library
>
> However, I got error when I tried CEAS: Enrichment on chromosome and annotation:
>  
> *****************************************************************************
> Dataset 23: CEAS: Enrichment on chromosome and annotation on data 16 and data 13
> The Galaxy framework encountered the following error while attempting to run the tool:
>  
> Traceback (most recent call last):
>   File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 121, in prepare_job
>     job_wrapper.prepare()
>   File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/jobs/__init__.py", line 707, in prepare
>     config_filenames = self.tool.build_config_files( param_dict, self.working_directory )
>   File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 2609, in build_config_files
>     f.write( fill_template( template_text, context=param_dict ) )
>   File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template
>     return str( Template( source=template_text, searchList=[context] ) )
>   File "/home/bioinfoadmin/app/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
>     return getattr(self, mainMethName)()
>   File "cheetah_DynamicallyCompiledCheetahTemplate_1391037616_15_43258.py", line 274, in respond
> NotFound: cannot find 'cistrome_static_library_path' while searching for '__app__.config.cistrome_static_library_path'
>  
> Tool execution generated the following error message:
>  
> failure preparing job
>  
> ********************************************************************************
>
> I'm quite confused since '__app__.config.cistrome_static_library_path' should be defined? or right now __app__ is dropped
> as Galaxy evolves? Besides, what does the comment mean by
>
> # Then in other tool configuration xml file, we can use 'from galaxy import config' then '$config.Configuration().cistrome_static_library_path'
>
> Does that mean that we should not be using __app__.config...but how to use this? I tried to insert
>
> 'from galaxy import config'
>
> into the xml file but only got error...
>
> I'll appreciate any input.
>
> Thanks,
> Rui
>
>
> ___________________________________________________________
> 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/