1) galaxy.yml
2) galaxy.ini
3) universe_wsgi.ini
Also:
- properly quote variables which may contain spaces
- no need to pass the config file to `./scripts/manage_tool_dependencies.py`
- simplify `scripts/maintenance.sh` by moving the `cd` up and reusing
functions from `scripts/common_startup_functions.sh`
to store --pid-file and --log-file options of `./scripts/paster.py` .
https://github.com/galaxyproject/galaxy/pull/6239 fixed 3 bugs:
- `GALAXY_RUN_ALL=1 ./run.sh` was reusing the same pid and log files for
all Galaxy processes;
- `./run.sh restart` was always using `paster.pid` and `paster.log` instead
of the configured files
- `./run.sh status` was always using `paster.pid`
but also introduced a regression, i.e. the plain `./run.sh` started
writing to the log file instead of the standard output (console).
This fixes the regression by using a separate variable for these options
instead of conflating them in `paster_args` or `server_args`.
dictConfig. Default log message format varies by stack.
- Refactor a lot of file extension handling in to galaxy.util.path.
- Simplify and improve config file finding.
- Simplify and improve native app creation.
- Integrate uWSGI argument generation with @jmchilton's improvements to
the startup scripts.
- Fix starting without a config file under uWSGI
- Implement kwalify schema to validate/define the schema.
- Replace ini configuration with YAML (completely backward compatible).
- Rebuild a sample configuration from the schema (config/reports.yml.sample).
- They now uniformly handle server option processing.
- Reports and Tool Shed now respect many new and important options such as --skip_venv.
- Reports and Tool Shed now do extra checking around Python version that Galaxy does.
In addition to improving the reports and tool shed startup scripts and reducing cognative load with respect to option handling, this is an important pre-condition to us being able us to switch on uwsgi by default for all three services simultaneously without a bunch of copy and pasting.
Do this by calling common_startup.sh prior to manage_db.sh in
run_test_wrapper.sh. Will require a rebuild of the testing-base image.
Also, have scripts in Galaxy root activate .venv if it exists.
Added flag (--sync-config) to run_reports.sh script that will cause it to synchronize the database connection and file path properties in reports_wsgi.ini with those in universe_wsgi.ini prior to starting paster app.
Allow specification of reports configuration directory mirroring similar extensions previously accepted for universe config and run.sh
Added usage documentation to run_reports.sh.
Added extension points to tweak pid and log location for reports application via environment variables.
Nate Coraor