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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