May 2022 Galaxy Release (v 22.05)

Get Galaxy

Highlights

The new History is the default History

See the 22.05 user release notes for details.

Galaxy is now exclusively a FastAPI application

As announced in the release notes for Galaxy Release 22.01 we have removed support to run Galaxy as a WSGI application. If you are still using uWSGI please consult the Migrating to Gunicorn documentation.

Deferred dataset resolution

Optional deferred dataset resolution enables users to select that datasets fetched from URLs or remote file sources should not be fetched into Galaxy’s objectstore. Deferred datasets are only fetched when jobs using these datasets are run.

Enhanced Celery tasks and features

Galaxy can optionally delegate the data upload job to Celery, and Galaxy can run the metadata script in Celery. This results in much shorter runtime for small jobs. To enable this, set enable_celery_tasks to true and ensure that at least one celery worker is started. If Celery tasks are enabled, it is also possible to change the datatype for many history items in batch.

Galaxy has a new database migrations system based on Alembic.

The new migrations system is built on top of Alembic. The SQLAlchemy Migrate tool has been retired. For usage, see Galaxy’s migrations documentation. For an architectural overview, see pull request #13108.

Also check out the 22.05 user release notes

Get Galaxy

The code lives at GitHub and you should have Git to obtain it.

To get a new Galaxy repository run:
$ git clone -b release_22.05 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
$ git fetch origin && git checkout release_22.05 && git pull --ff-only origin release_22.05

See the community hub for additional details on source code locations.

Configuration Changes

Added

The following configuration options are new

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.celery_backend

  • mapping.galaxy.mapping.celery_broker

  • mapping.galaxy.mapping.display_builtin_converters

  • mapping.galaxy.mapping.file_sources

  • mapping.galaxy.mapping.helpsite_url

  • mapping.galaxy.mapping.log_destination

  • mapping.galaxy.mapping.log_rotate_count

  • mapping.galaxy.mapping.log_rotate_size

  • mapping.galaxy.mapping.prefer_custos_login

  • mapping.galaxy.mapping.short_term_storage_cleanup_interval

  • mapping.galaxy.mapping.short_term_storage_default_duration

  • mapping.galaxy.mapping.short_term_storage_dir

  • mapping.galaxy.mapping.short_term_storage_maximum_duration

  • mapping.galaxy.mapping.tool_help_bm25f_k1

  • mapping.galaxy.mapping.tool_name_exact_multiplier

  • mapping.galaxy.mapping.tool_ngram_factor

  • mapping.galaxy.mapping.use_legacy_history

  • mapping.galaxy.mapping.workflow_monitor_sleep

Changed

The following configuration options have been changed

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.debug.desc has changed from

    Debug enables access to various config options useful for development
and debugging: use_lint, use_profile, and use_printdebug.  It also
causes the files used by PBS/SGE (submission script, output, and error)
to remain on disk after the job is complete.

In addition, this will set uWSGI's `honour-stdin` option to `true`;
thus, preventing uWSGI from remapping stdin to `/dev/null` and
enabling debugging with tools like pdb. To keep uWSGI's default
setting, set `honor-stdin` to `false` in the `uwsgi` section of this
configuration file.

    to

    Debug enables access to various config options useful for development
and debugging: use_lint, use_profile, and use_printdebug.  It also
causes the files used by PBS/SGE (submission script, output, and error)
to remain on disk after the job is complete.

  • mapping.galaxy.mapping.logging.desc has changed from

    Controls where and how the server logs messages. If unset, the default is to log all messages to standard
output at the level defined by the `log_level` configuration option. Configuration is described in the
documentation at:
https://docs.galaxyproject.org/en/master/admin/config_logging.html

    to

    Controls where and how the server logs messages. If set, overrides all settings in the log_* configuration
options. Configuration is described in the documentation at:
https://docs.galaxyproject.org/en/master/admin/config_logging.html

  • mapping.galaxy.mapping.metadata_strategy.desc has changed from

    Determines how metadata will be set. Valid values are `directory` and `extended`.
In extended mode jobs will decide if a tool run failed, the object stores
configuration is serialized and made available to the job and is used for
writing output datasets to the object store as part of the job and dynamic
output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
etc) happens as part of the job.

    to

    Determines how metadata will be set. Valid values are `directory`, `extended`,
`directory_celery` and `extended_celery`.
In extended mode jobs will decide if a tool run failed, the object stores
configuration is serialized and made available to the job and is used for
writing output datasets to the object store as part of the job and dynamic
output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
etc) happens as part of the job. In `directory_celery` and `extended_celery` metadata
will be set within a celery task.

  • mapping.galaxy.mapping.screencasts_url.default has changed from

    https://vimeo.com/galaxyproject

    to

    https://www.youtube.com/c/galaxyproject

  • mapping.galaxy.mapping.simplified_workflow_run_ui_target_history.default has changed from

    current

    to

    prefer_current

  • mapping.galaxy.mapping.simplified_workflow_run_ui_target_history.desc has changed from

    When the simplified workflow run form is rendered, should the invocation outputs
be sent to the 'current' history or a 'new' history.

    to

    When the simplified workflow run form is rendered, should the invocation outputs
be sent to the 'current' history or a 'new' history. If the user should be presented
and option between these - set this to 'prefer_current' or 'prefer_new' to display
a runtime setting with the corresponding default. The default is to provide the
user this option and default it to the current history (the traditional behavior
of Galaxy for years) - this corresponds to the setting 'prefer_current'.

  • mapping.galaxy.mapping.simplified_workflow_run_ui_target_history.enum has changed from

    current
new

    to

    current
new
prefer_current
prefer_new

  • mapping.galaxy.mapping.tool_description_boost.default has changed from

    2.0

    to

    8.0

  • mapping.galaxy.mapping.tool_description_boost.desc has changed from

    Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

    to

    In tool search, a query match against a tool's description text will
receive this score multiplier.

  • mapping.galaxy.mapping.tool_enable_ngram_search.desc has changed from

    Enable/ disable Ngram-search for tools. It makes tool
search results tolerant for spelling mistakes in the query
by dividing the query into multiple ngrams and search for
each ngram

    to

    Disabling this will prevent partial matches on tool names.
Enable/disable Ngram-search for tools. It makes tool
search results tolerant for spelling mistakes in the query, and will
also match query substrings e.g. "genome" will match "genomics" or
"metagenome".

  • mapping.galaxy.mapping.tool_help_boost.default has changed from

    0.5

    to

    1.0

  • mapping.galaxy.mapping.tool_help_boost.desc has changed from

    Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

    to

    In tool search, a query match against a tool's help text will receive
this score multiplier.

  • mapping.galaxy.mapping.tool_id_boost.default has changed from

    9.0

    to

    20.0

  • mapping.galaxy.mapping.tool_id_boost.desc has changed from

    Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

    to

    In tool search, a query match against a tool's ID text will receive
this score multiplier. The query must be an exact match against ID
in order to be counted as a match.

  • mapping.galaxy.mapping.tool_label_boost.desc has changed from

    Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

    to

    In tool search, a query match against a tool's label text will
receive this score multiplier.

  • mapping.galaxy.mapping.tool_name_boost.default has changed from

    9.0

    to

    20.0

  • mapping.galaxy.mapping.tool_name_boost.desc has changed from

    Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

    to

    In tool search, a query match against a tool's name text will receive
this score multiplier.

  • mapping.galaxy.mapping.tool_ngram_maxsize.desc has changed from

    Set maximum size of ngrams

    to

    Set maximum character length of ngrams

  • mapping.galaxy.mapping.tool_ngram_minsize.desc has changed from

    Set minimum size of ngrams

    to

    Set minimum character length of ngrams

  • mapping.galaxy.mapping.tool_search_limit.desc has changed from

    Limits the number of results in toolbox search.  Can be used to tweak how many
results will appear.

    to

    Limits the number of results in toolbox search. Use to set the
maximum number of tool search results to display.

  • mapping.galaxy.mapping.tool_section_boost.desc has changed from

    Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

    to

    In tool search, a query match against a tool's section text will
receive this score multiplier.

  • mapping.galaxy.mapping.tool_stub_boost.default has changed from

    5.0

    to

    2.0

  • mapping.galaxy.mapping.tool_stub_boost.desc has changed from

    Boosts are used to customize this instance's toolbox search.
The higher the boost, the more importance the scoring algorithm gives to the
given field.  Section refers to the tool group in the tool panel.  Rest of
the fields are tool's attributes.

    to

    A stub is parsed from the GUID as "owner/repo/tool_id".
In tool search, a query match against a tool's stub text will receive
this score multiplier.

  • mapping.galaxy.mapping.wiki_url.desc has changed from

    The URL linked by the "Wiki" link in the "Help" menu.

    to

    The URL linked by the "Community Hub" link in the "Help" menu.

Removed

The following configuration options have been completely removed

config/tool_shed.yml.sample

  • uwsgi

config/galaxy.yml.sample

  • uwsgi

config/reports.yml.sample

  • uwsgi

config/galaxy.yml.sample:galaxy

  • mapping.galaxy.mapping.containers_config_file

  • mapping.galaxy.mapping.enable_beta_containers_interface

  • mapping.galaxy.mapping.interactive_environment_plugins_directory

  • mapping.galaxy.mapping.mailing_lists_url

  • mapping.galaxy.mapping.qa_url

  • mapping.galaxy.mapping.search_url

Release Notes

Enhancements

Fixes

To stay up to date with Galaxy’s progress, watch our screencasts; visit our community Hub; and follow us on Bluesky, Mastodon, and LinkedIn.

You can always chat with us on Matrix.

Thanks for using Galaxy!

The Galaxy Team