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Undefined layout variable errors #111

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natefoo opened this issue Mar 24, 2020 · 0 comments
Open

Undefined layout variable errors #111

natefoo opened this issue Mar 24, 2020 · 0 comments
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@natefoo
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natefoo commented Mar 24, 2020

@vazovn reported an issue on Gitter with the layout set to root-dir and tool_dependency_dir set in galaxy_config.galaxy, that attempting to use galaxy_tool_dependency_dir in another var (miniconda_prefix) was causing the error:

FAILED! => {"msg": "The conditional check ''galaxy_' ~ item in vars and item in ((galaxy_config | default({}))[galaxy_app_config_section] | default({}))' failed. The error was: error while evaluating conditional ('galaxy_' ~ item in vars and item in ((galaxy_config | default({}))[galaxy_app_config_section] | default({}))): 'galaxy_tool_dependency_dir' is undefined\n\nThe error appears to be in '/uio/kant/usit-ft-u1/nikolaiv/galaxy-ImmunoHub-playbooks/roles/galaxyproject.galaxy/tasks/layout.yml': line 21, column 3, but may\nbe elsewhere in the file depending on the exact syntax problem.\n\nThe offending line appears to be:\n\n\n- name: Check that any explicitly set Galaxy config options match the values of explicitly set variables\n ^ here\n"}

Adding galaxy_tool_dependency_dir to the Set any unset variables from layout defaults task fixes this. I am not sure why the vars in the last 2 tasks of tasks/layout.yml aren't defaulted in the "Set any unset..." task, but if there's no reason not to, we should default them there.

@hexylena hexylena added the bug label Jul 14, 2020
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