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"shed_tool_conf.xml.sample" is located inside config directory. Only seems logical that "shed_tool_conf.xml" should be in config also.
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@@ -136,7 +136,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
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# Tools can be locally developed or installed from Galaxy tool sheds.
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# (config/tool_conf.xml.sample will be used if left unset and
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# config/tool_conf.xml does not exist).
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#tool_config_file = config/tool_conf.xml,shed_tool_conf.xml
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#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
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# Enable / disable checking if any tools defined in the above non-shed tool_config_files
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# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool
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