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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