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 <ruiwang.sz@gmail.com> 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

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