[galaxy-dev] Tool config Cheetah errors

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[galaxy-dev] Tool config Cheetah errors

Nate Coraor (nate@bx.psu.edu)
Hi Amit,

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Modi, Amit wrote:
 >     Hi,
 >
 >     I have added a few tools in the galaxy.For one of these tools it
 >     sometime gives an error.
 >     but everytime I execute this tool it renders this exception on
console.
 >
 >     Can anybody please help me fix it.
 >
 >     galaxy.jobs DEBUG 2010-05-21 14:30:03,166 dispatching job 203 to sge
 >     runner
 >     galaxy.jobs.runners.sge ERROR 2010-05-21 14:30:03,508 failure
 >     running job 203
 >     Traceback (most recent call last):
 >       File
 >     "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/sge.py",
 >     line 120, in queue_job
 >         job_wrapper.prepare()
 >       File
 >     "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
 >     390, in prepare
 >         self.command_line = self.tool.build_command_line( param_dict )
 >       File
 >     "/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line
 >     1343, in build_command_line
 >         command_line = fill_template( self.command, context=param_dict )
 >       File
 >     "/export/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line
 >     9, in fill_template
 >         return str( Template( source=template_text,
searchList=[context] ) )
 >       File
 >
"/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
 >     line 1244, in __init__
 >         self._compile(source, file, compilerSettings=compilerSettings)
 >       File
 >
"/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
 >     line 1538, in _compile
 >         keepRefToGeneratedCode=True)
 >       File
 >
"/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
 >     line 745, in compile
 >         compiler.compile()
 >       File
 >
"/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Compiler.py",
 >     line 1670, in compile
 >         self._parser.parse()
 >       File
 >
"/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py",
 >     line 1488, in parse
 >         self.eatDirective()
 >       File
 >
"/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py",
 >     line 1610, in eatDirective
 >         directiveParser()
 >       File
 >
"/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py",
 >     line 1755, in eatEndDirective
 >         raise ParseError(self, msg='Invalid end directive')
 >     ParseError:
 >
 >     Invalid end directive
 >     Line 3, column 6
 >
 >     Line|Cheetah Code
 >     ----|-------------------------------------------------------------
 >     2   |    #else: #gkelvin $confile.nonmeta
 >     3   |    #end
 >               ^
 >     4   |
 >
 >     galaxy.jobs DEBUG 2010-05-21 14:30:03,509 job 203 dispatched


The closing syntax for an 'if' statement in Cheetah is:

#end if

Also, the : is not necessary after the 'else' statement, and I believe
it's deprecated.

--nate

 >
 >
 >     Regards,
 >     Amit Modi
 >
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