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Enable Galaxy outputs_to_working_directory by default #1199

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merged 5 commits into from
May 16, 2022
Merged

Enable Galaxy outputs_to_working_directory by default #1199

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5b41e32
let Galaxy use output_to_working dir
bernt-matthias Oct 22, 2021
13c4f21
add comment and fix linting
bernt-matthias Oct 22, 2021
9e156db
remove TODO
bernt-matthias Oct 22, 2021
4b699cb
fix lint error
bernt-matthias Oct 22, 2021
6a072fe
Merge branch 'master' into topic/output_to_working_dir
bernt-matthias May 16, 2022
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2 changes: 1 addition & 1 deletion planemo/galaxy/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -484,6 +484,7 @@ def config_join(*args):
migrated_tools_config=empty_tool_conf,
test_data_dir=test_data_dir, # TODO: make gx respect this
shed_data_manager_config_file=shed_data_manager_config_file,
outputs_to_working_directory="True", # this makes Galaxy's files dir RO for dockerized testing
)
)
_handle_container_resolution(ctx, kwds, properties)
Expand All @@ -500,7 +501,6 @@ def config_join(*args):
# sanitize_all_html = True
# serve_xss_vulnerable_mimetypes = False
# track_jobs_in_database = None
# outputs_to_working_directory = False
# retry_job_output_collection = 0

env = _build_env_for_galaxy(properties, template_args)
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