Skip to content

Enable Galaxy outputs_to_working_directory by default #1199

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
nsoranzo merged 5 commits into from
May 16, 2022
Merged

Enable Galaxy outputs_to_working_directory by default #1199

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion planemo/galaxy/config.py
View file
Open in desktop
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)
Expand Down