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...@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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