A process manager (supervisor) and management tools for Galaxy servers.
Installing this will give you two executables, galaxyctl which is used to manage the starting, stopping, and logging
of Galaxy's various processes, and galaxy, which can be used to run a Galaxy server in the foreground.
Python 3.7 or later is required. Gravity can be installed independently of Galaxy, but please read the section on Galaxy Integration below.
To install:
$ pip install gravity
To make your life easier, you are encourged to install into a virtualenv. The easiest way to do this is with Python's built-in venv module:
$ python3 -m venv ~/gravity $ . ~/gravity/bin/activate
By default, Gravity will store its state, configuration, and log files in $XDG_CONFIG_HOME/galaxy-gravity, where
$XDG_CONFIG_HOME typically defaults to ~/.config. You can change this with the --state-dir option to the
Gravity commands, or by setting $GRAVITY_STATE_DIR in your environment.
Gravity was originally designed to support managing multiple Galaxy (as well as Galaxy Reports and Tool Shed) servers on a single host, but hides some of this complexity from you if you are working with a single Galaxy server. Additionally, Galaxy 22.01 has added Gravity as a dependency, and changes have been made to Gravity to support this mode of operation.
- Gravity 0.9.0 has dropped support for running Galaxy with uWSGI in favor of gunicorn and FastAPI.
- Gravity 0.9.0 cannot be used with Galaxy versions older than 22.01.
- As of Galaxy 22.01, Gravity is automatically installed into Galaxy's virtualenv by Galaxy's setup scripts (as called
by
run.sh) - Galaxy's setup scripts as of 22.01 also set
$GRAVITY_STATE_DIRto<galaxy_root>/database/gravitywhen running Galaxy from the source directory. This keeps each Galaxy instance's Gravity configuration separate.
If running from the root of a Galaxy source tree, you can start and run Galaxy in the foreground with:
$ galaxy Registered galaxy config: /home/nate/work/galaxy/config/galaxy.yml Creating or updating service gunicorn Creating or updating service celery Creating or updating service celery-beat celery: added process group 2022-01-20 14:44:24,619 INFO spawned: 'celery' with pid 291651 celery-beat: added process group 2022-01-20 14:44:24,620 INFO spawned: 'celery-beat' with pid 291652 gunicorn: added process group 2022-01-20 14:44:24,622 INFO spawned: 'gunicorn' with pid 291653 celery STARTING celery-beat STARTING gunicorn STARTING ==> /home/nate/work/galaxy/database/gravity/log/gunicorn.log <== ...log output follows...
Galaxy will continue to run and output logs to stdout until terminated with CTRL+C.
The galaxy command is actually a shortcut for three separate steps: 1. register your Galaxy configuration file
(galaxy.yml) with Gravity, 2. write out the process manager configurations, and 3. start and run Galaxy in the
foreground using the process manager (supervisor). You can perform these steps separately (and in this example, start
Galaxy as a backgrounded daemon instead of in the foreground):
$ galaxyctl register config/galaxy.yml Registered galaxy config: /home/nate/work/galaxy/config/galaxy.yml $ galaxyctl update Creating or updating service gunicorn Creating or updating service celery Creating or updating service celery-beat $ galaxyctl start celery STARTING celery-beat STARTING gunicorn STARTING Log files are in /home/nate/work/galaxy/database/gravity/log
When running as a daemon, the stop subcommand stops your Galaxy server:
$ galaxyctl stop celery-beat: stopped gunicorn: stopped celery: stopped All processes stopped, supervisord will exit Shut down
Once a Galaxy configuration file has been registered with Gravity, it doesn't matter where you call galaxy or
galaxyctl from.
The following options in the gravity section of galaxy.yml can be used to control Gravity::
unset are shown):
# Configuration for Gravity process manager.
# ``uwsgi:`` section will be ignored if Galaxy is started via Gravity commands (e.g ``./run.sh``, ``galaxy`` or ``galaxyctl``).
gravity:
# Specify Galaxy's root directory.
# Gravity will attempt to find the root directory, but you can set the directory explicitly with this option.
# galaxy_root:
# Set to a directory that should contain log files for the processes controlled by Gravity.
# If not specified defaults to ``<state_dir>/log``.
# log_dir:
# Set to Galaxy's virtualenv directory.
# If not specified, Gravity assumes all processes are on PATH.
# virtualenv:
# Select the application server.
# ``gunicorn`` is the default application server.
# ``unicornherder`` is a production-oriented manager for (G)unicorn servers that automates zero-downtime Galaxy server restarts,
# similar to uWSGI Zerg Mode used in the past.
# Valid options are: gunicorn, unicornherder
# app_server: gunicorn
# Override the default instance name.
# this is hidden from you when running a single instance.
# instance_name: _default_
# Configuration for Gunicorn.
gunicorn:
# Enable Galaxy gunicorn server.
# enable: true
# The socket to bind. A string of the form: ``HOST``, ``HOST:PORT``, ``unix:PATH``, ``fd://FD``. An IP is a valid HOST.
# bind: localhost:8080
# Controls the number of Galaxy application processes Gunicorn will spawn.
# Increased web performance can be attained by increasing this value.
# If Gunicorn is the only application on the server, a good starting value is the number of CPUs * 2 + 1.
# 4-12 workers should be able to handle hundreds if not thousands of requests per second.
# workers: 1
# Gunicorn workers silent for more than this many seconds are killed and restarted.
# Value is a positive number or 0. Setting it to 0 has the effect of infinite timeouts by disabling timeouts for all workers entirely.
# If you disable the ``preload`` option workers need to have finished booting within the timeout.
# timeout: 300
# Extra arguments to pass to Gunicorn command line.
# extra_args:
# Use Gunicorn's --preload option to fork workers after loading the Galaxy Application.
# Consumes less memory when multiple processes are configured. Default is ``false`` if using unicornherder, else ``true``.
# preload:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
# Configuration for Celery Processes.
celery:
# Enable Celery distributed task queue.
# enable: true
# Enable Celery Beat periodic task runner.
# enable_beat: true
# Number of Celery Workers to start.
# concurrency: 2
# Log Level to use for Celery Worker.
# Valid options are: DEBUG, INFO, WARNING, ERROR
# loglevel: DEBUG
# Queues to join
# queues: celery,galaxy.internal,galaxy.external
# Pool implementation
# Valid options are: prefork, eventlet, gevent, solo, processes, threads
# pool: threads
# Extra arguments to pass to Celery command line.
# extra_args:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
# Configuration for gx-it-proxy.
gx_it_proxy:
# Set to true to start gx-it-proxy
# enable: false
# Public-facing IP of the proxy
# ip: localhost
# Public-facing port of the proxy
# port: 4002
# Routes file to monitor.
# Should be set to the same path as ``interactivetools_map`` in the ``galaxy:`` section.
# sessions: database/interactivetools_map.sqlite
# Include verbose messages in gx-it-proxy
# verbose: true
# Forward all requests to IP.
# This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
# forward_ip:
# Forward all requests to port.
# This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
# forward_port:
# Rewrite location blocks with proxy port.
# This is an advanced option that is only needed when proxying to remote interactive tool container that cannot be reached through the local network.
# reverse_proxy: false
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
# Configuration for tusd server (https://github.com/tus/tusd).
# The ``tusd`` binary must be installed manually and made available on PATH (e.g in galaxy's .venv/bin directory).
tusd:
# Enable tusd server.
# If enabled, you also need to set up your proxy as outlined in https://docs.galaxyproject.org/en/latest/admin/nginx.html#receiving-files-via-the-tus-protocol.
# enable: false
# Path to tusd binary
# tusd_path: tusd
# Host to bind the tusd server to
# host: localhost
# Port to bind the tusd server to
# port: 1080
# Directory to store uploads in.
# Must match ``tus_upload_store`` setting in ``galaxy:`` section.
# upload_dir:
# Comma-separated string of enabled tusd hooks.
#
# Leave at the default value to require authorization at upload creation time.
# This means Galaxy's web process does not need to be running after creating the initial
# upload request.
#
# Set to empty string to disable all authorization. This means data can be uploaded (but not processed)
# without the Galaxy web process being available.
#
# You can find a list of available hooks at https://github.com/tus/tusd/blob/master/docs/hooks.md#list-of-available-hooks.
# hooks_enabled_events: pre-create
# Extra arguments to pass to tusd command line.
# extra_args:
# Extra environment variables and their values to set when running the service. A dictionary where keys are the variable
# names.
# environment: {}
# Configure dynamic handlers in this section.
# See https://docs.galaxyproject.org/en/latest/admin/scaling.html#dynamically-defined-handlers for details.
# handlers: {}
As a convenience for cases where you may want to have different Gravity configurations but a single Galaxy configuration (e.g. your Galaxy server is split across multiple hosts), the Gravity configuration can be stored in a separate file and included into the Galaxy configuration. For example, on a deployment where the web (gunicorn) and job handler processes run on different hosts, one might have:
In galaxy.yml:
gravity: !include gravity.yml galaxy: database_connection: postgresql://... ...
In gravity.yml on the web host:
log_dir: /var/log/galaxy gunicorn: bind: localhost:8888 celery: enable: false enable_beat: false
In gravity.yml on the job handler host:
log_dir: /var/log/galaxy
gunicorn:
enable: false
celery:
enable: true
enable_beat: true
handlers:
handler:
processes: 2
Gravity has support for reading Galaxy's job configuration: it can read statically configured job handlers in the
job_conf.yml or job_conf.yml files, or the job configuration inline from the job_config option in
galaxy.yml. However, unless you need to statically define handlers, it is simpler to configure Gravity to run
dynamically defined handlers as detailed in the Galaxy scaling documentation.
When using dynamically defined handlers, be sure to explicitly set the job handler assignment method to
db-skip-locked or db-transaction-isolation to prevent the web process from also handling jobs.
Gravity's configuration is defined in Galaxy's configuration file to be easy and familiar for Galaxy administrators, but
Gravity maintains its own state in $GRAVITY_STATE_DIR/configstate.yaml. If set, the options in galaxy.yml
will override Gravity's saved state whenever galaxyctl update is run, but if later unset, then the persisted
values in Gravity's saved state are used.
The exception is the values of app_server and job_handler_*, which will revert to default values if unset in
galaxy.yml, because Gravity dynamically adds and removes services based on the Galaxy configuration by design.
Use galaxyctl --help for help. Subcommands also support --help, e.g. galaxy register --help
Register a Galaxy server config (galaxy.yml) with Gravity. Does not update or start. Run galaxyctl update after
registering to apply changes.
List config files registered with the process manager.
Deregister a Galaxy server config, Gravity will no longer manage this Galaxy instance. Run galaxyctl update after
deregistering to apply changes.
Start and run Galaxy and associated processes in daemonized (background) mode, or -f to run in the foreground and
follow log files. The galaxy command is a shortcut for galaxyctl start -f.
If no config files are registered and you run galaxyctl start from the root of a Galaxy source tree, it
automatically runs the equivalent of:
$ galaxyctl register config/galaxy.yml # or galaxy.yml.sample if galaxy.yml does not exist $ galaxyctl update $ galaxyctl start
Stop daemonized Galaxy server processes. If no processes remain running after this step (which should be the case when
working with a single Galaxy instance), supervisord will terminate.
Restart Galaxy server processes. This is done in a relatively "brutal" fashion: processes are signaled (by supervisor)
to exit, and then are restarted. See the graceful subcommand to restart gracefully.
Restart Galaxy with minimal interruption. If running with gunicorn this means holding the web socket open while restarting (connections to Galaxy will block). If running with unicornherder, a new Galaxy application will be started and the old one shut down only once the new one is accepting connections. A graceful restart with unicornherder should be transparent to clients.
Figure out what has changed in configs, which could be:
- changes to the Gravity configuration options in
galaxy.yml - adding or removing handlers in
job_conf.xml
This may cause service restarts if there are any changes.
Any needed changes to supervisor configs will be performed and then supervisorctl update will be called.
update is called automatically for the start, stop, restart, and graceful subcommands.
Stop all processes and cause supervisord to terminate. Similar to stop but there is no ambiguity as to whether
supervisord remains running.
Pass through directly to supervisor. Run galaxyctl supervisorctl to invoke the supervisorctl shell, or galaxyctl
supervisorctl [command] to call a supervisorctl command directly. See the supervisor documentation or galaxyctl
supervisorctl help for help.
List known (configured) Galaxy instances and services.
Show stored configuration details for the named config file.
If your galaxy.yml has moved, you can update its path in Gravity's saved state with this command.
As discussed in the Configuration section, Gravity maintains a state file that also acts as a configuration of sorts.
Administrators deploying Galaxy with a deployment tool (e.g. Ansible) can take advantage of this to deploy a Gravity
state file as part of their Galaxy deployment. See the $GRAVITY_STATE_DIR/configstate.yaml file after performing a
register and update command to see what this file looks like, or below for an example. Keep in mind that running
galaxyctl commands after changing the Galaxy configuration can cause changes to the state file because it was not
originally intended to be user-maintainable. See Issue #6 for discussion and development related to this, as we seek
to provide a more consistent experience in working with Gravity's configuration.
A configstate.yaml file for a Galaxy service might look like:
config_files:
/home/nate/work/galaxy/config/galaxy.yml:
config_type: galaxy
instance_name: _default_
attribs:
app_server: gunicorn
log_dir: /home/nate/work/galaxy/database/gravity/log
bind: 'localhost:8080'
galaxy_root: /home/nate/work/galaxy
services:
- config_type: galaxy
service_type: gunicorn
service_name: gunicorn
- config_type: galaxy
service_type: celery
service_name: celery
- config_type: galaxy
service_type: celery-beat
service_name: celery-beat