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ToolShed tool dependency install fixes #4105

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merged 3 commits into from May 23, 2017

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commented May 23, 2017

See individual commits for details.

nsoranzo added some commits May 22, 2017

Catch specific exception type
Also remove unused variable
Allow empty <environment_variable>
Presently trying to install a ToolShed tool dependency defined as

<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="MYVAR" action="set_to"></environment_variable>
    </set_environment>
</tool_dependency>

results in EnvManager.create_env_var_dict() returning None, which in turn
causes the dependency silently not being installed with this error in the
logs:

tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler DEBUG 2017-05-23 10:08:23,798 Error setting environment for tool dependency: local variable 'tool_dependency' referenced before assignment
Raise an exception if name or action are not defined
instead of silently skipping the <environment_variable> tool dependency

@mvdbeek mvdbeek merged commit 2aec5dd into galaxyproject:dev May 23, 2017

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@mvdbeek

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commented May 23, 2017

Thanks for digging into this @nsoranzo !

@nsoranzo nsoranzo deleted the nsoranzo:ts_tool_dep_install_fixes branch May 25, 2017

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