Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 47339bf1f33b52fade0db00a1af23eba34648da5 https://github.com/galaxyproject/galaxy/commit/47339bf1f33b52fade0db00a1af23... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-05-22 (Mon, 22 May 2017)

Changed paths: M lib/tool_shed/galaxy_install/install_manager.py

Log Message: ----------- Catch specific exception type

Also remove unused variable

Commit: a033a5821ad11fbe0465b01984c97e591785623c https://github.com/galaxyproject/galaxy/commit/a033a5821ad11fbe0465b01984c97... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-05-23 (Tue, 23 May 2017)

Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py

Log Message: ----------- 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

Commit: e4de203c7da50aee3a95edacaf7f00d79b1ac416 https://github.com/galaxyproject/galaxy/commit/e4de203c7da50aee3a95edacaf7f0... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2017-05-23 (Tue, 23 May 2017)

Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py

Log Message: ----------- Raise an exception if name or action are not defined

instead of silently skipping the <environment_variable> tool dependency

Commit: 2aec5dda9ad7b66b0da6de08873b919d472b0309 https://github.com/galaxyproject/galaxy/commit/2aec5dda9ad7b66b0da6de08873b9... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2017-05-23 (Tue, 23 May 2017)

Changed paths: M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py

Log Message: ----------- Merge pull request #4105 from nsoranzo/ts_tool_dep_install_fixes

ToolShed tool dependency install fixes

Compare: https://github.com/galaxyproject/galaxy/compare/1bc8ea69c950...2aec5dda9ad7