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Replacement should be applied only to first occurrence.
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@@ -54,7 +54,7 @@ def verify_tools( app, url, galaxy_config_file, engine_options={} ):
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break
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config_arg = ''
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if os.path.abspath( os.path.join( os.getcwd(), 'galaxy.ini' ) ) != galaxy_config_file:
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config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' )
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config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.', 1 )
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if not app.config.running_functional_tests:
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if tool_shed_accessible:
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# Automatically update the value of the migrate_tools.version database table column.
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