Setup forcing export of format2 workflows by default in next release. There should be a least one release between enabling them to be imported by default and exporting them by default anyway I think - so 19.09 workflows can still be used on slightly older Galaxy instances.
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
- 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.
- Populate test server with demo webhooks by default.
- Eliminate special logic needed to treat the demo directory differently.
- Document how to enable the demo webhooks in galaxy.ini.sample.
- Populate the demo webhooks when starting Galaxy with GALAXY_RUN_WITH_TEST_TOOLS=1 set.
- Construct a DependencyManager according to Galaxy's configuration before Galaxy starts to allow auto installation of Conda.
- Add script for managing tool dependencies outside of a Galaxy environment.
- Refactor to allow this to be done without duplicating logic related to defaults, configuration handling, etc....
Implements #3426.
management. Drop hard requirement on lzo (doubt anyone other than
usegalaxy.org is using it, but it will be added as a extras option for
bxlab/bx-python for anyone who is).
Fixes#1150
Start Galaxy using
GALAXY_RUN_WITH_TEST_TOOLS=1 run.sh
Enables beta tool formats (e.g. YAML, and CWL downstream), beta workflow modules, and the suite of Galaxy test tools used by testing framework.
Also add the following combination:
GALAXY_RUN_ALL=1 ./run.sh --daemon --wait
which, by preventing servers from starting simultaneously, is useful when
multiple servers are configured before creating the database, or when updating
to a new Galaxy release containing a database upgrade.
GALAXY_UNIVERSE_CONFIG_DIR. If this is set, before Galaxy is launched
the directory specified by the environment variable is searched for
ini config files. These files are merged into a single configuration
structure and written back out as universe.ini.
This should allow for a more modular configuration of Galaxy. The
files are merged in lexiographic order and later files can override
properties specified ealier on. If a consistent naming scheme is used
this can be really useful:
As an example, one might specify the files as such:
000_galaxy_defaults.ini
000_default_sqlite_config.ini
100_institution_specific.ini
500_job_runner.ini
500_webapp_0.ini
500_webapp_1.ini
500_instance_specific.ini
500_available_postgres.ini
Nicola Soranzo