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 =

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


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):

line 121, in prepare_job


  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] ) )

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

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.

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