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mvdbeek f16e7fcec4 watch tool source stores: poll freshness, reload on CVMFS publish 
New opt-in watch_tool_source_stores (+ tool_source_store_watch_interval,
default 60s): a per-process thread polls the freshness probe of every
read-only named store — one extended-attribute read per store per tick
for CVMFS — and reacts to token transitions. inotify does not fire on
CVMFS, so polling is the only reliable signal, and catalog TTL bounds
propagation anyway.

On a transition the store's engine is disposed before the index reload:
CVMFS keeps serving the pre-publish file to descriptors that were open
before the catalog update, so pooled sqlite connections pin the old
snapshot until dropped. The same disposal now also runs for read-only
members in invalidate_index_cache, making the existing admin reload API
and reload_tool_source_cache broadcasts correct on CVMFS as the manual
trigger. The reload itself reuses invalidate_index_cache (stub
registration, removal reconcile) plus a per-changed-store whoosh rebuild
guarded by the corpus-signature skip.

Watchable stores are read-only members with a probe: writable stores
change through this process group's own populate paths, which already
broadcast their own reloads. The watcher compares against the last
*seen* token, not the persisted one, so a store whose publisher hasn't
repopulated yet logs once instead of re-firing every tick.

Claude-Session: https://claude.ai/code/session_018L7ZmCv2ubKA3JNeSL8Pkr
2026-07-28 17:27:30 +02:00

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~~~~~~~~~~~~~~
``config_dir``
~~~~~~~~~~~~~~
:Description:
The directory that will be prepended to relative paths in options
specifying other Galaxy config files (e.g. datatypes_config_file).
Defaults to the directory in which galaxy.yml is located.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``managed_config_dir``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
The directory that will be prepended to relative paths in options
specifying config files controlled by Galaxy (such as
shed_tool_config_file, etc.). Must be writable by the user running
Galaxy. Defaults to `<config_dir>/` if running Galaxy from source
or `<data_dir>/config` otherwise.
:Default: ``None``
:Type: str
~~~~~~~~~~~~
``data_dir``
~~~~~~~~~~~~
:Description:
The directory that will be prepended to relative paths in options
specifying Galaxy data/cache directories and files (such as the
default SQLite database, file_path, etc.). Defaults to `database/`
if running Galaxy from source or `<config_dir>/data` otherwise.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~
``templates_dir``
~~~~~~~~~~~~~~~~~
:Description:
The directory containing custom templates for Galaxy, such as
HTML/text email templates. Defaults to 'templates'. Default
templates can be found in the Galaxy root under config/templates.
These can be copied to <templates_dir> if you wish to customize
them.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``templates``
:Type: str
~~~~~~~~~~~~~
``cache_dir``
~~~~~~~~~~~~~
:Description:
Top level cache directory. Any other cache directories
(template_cache_path, etc.) should be subdirectories.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``cache``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``database_connection``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
By default, Galaxy uses a SQLite database at
'<data_dir>/universe.sqlite'. You may use a SQLAlchemy connection
string to specify an external database instead.
Sample default
'sqlite:///<data_dir>/universe.sqlite?isolation_level=IMMEDIATE'
You may specify additional options that will be passed to the
SQLAlchemy database engine by using the prefix
"database_engine_option_". For some of these options, default
values are provided (e.g. see database_engine_option_pool_size,
etc.).
The same applies to `install_database_connection`, for which you
should use the "install_database_engine_option_" prefix.
For more options, please check SQLAlchemy's documentation at
https://docs.sqlalchemy.org/en/14/core/engines.html?highlight=create_engine#sqlalchemy.create_engine
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_engine_option_pool_size``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If the server logs errors about not having enough database pool
connections, you will want to increase these values, or consider
running more Galaxy processes.
:Default: ``5``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_engine_option_max_overflow``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If the server logs errors about not having enough database pool
connections, you will want to increase these values, or consider
running more Galaxy processes.
:Default: ``10``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_engine_option_pool_recycle``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If using MySQL and the server logs the error "MySQL server has
gone away", you will want to set this to some positive value (7200
should work).
:Default: ``-1``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_engine_option_server_side_cursors``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If large database query results are causing memory or response
time issues in the Galaxy process, leave the result on the server
instead. This option is only available for PostgreSQL and is
highly recommended.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_query_profiling_proxy``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Log all database transactions, can be useful for debugging and
performance profiling. Logging is done via Python's 'logging'
module under the qualname
'galaxy.model.orm.logging_connection_proxy'
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``database_template``
~~~~~~~~~~~~~~~~~~~~~
:Description:
If auto-creating a postgres database on startup - it can be based
on an existing template database. This will set that. This is
probably only useful for testing but documentation is included
here for completeness.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_log_query_counts``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Log number of SQL queries executed and total time spent
dispatching SQL statements for each web request. If statsd is also
enabled this information will be logged there as well. This should
be considered somewhat experimental, we are unsure of the
performance costs of running this in production. This is useful
information for optimizing database interaction performance.
Similar information can be obtained on a per-request basis by
enabling the sql_debug middleware and adding sql_debug=1 to a
request string.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``slow_query_log_threshold``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Slow query logging. Queries slower than the threshold indicated
below will be logged to debug. A value of '0' is disabled. For
example, you would set this to .005 to log all queries taking
longer than 5 milliseconds.
:Default: ``0.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_per_request_sql_debugging``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enables a per request sql debugging option. If this is set to
true, append ?sql_debug=1 to web request URLs to enable detailed
logging on the backend of SQL queries generated during that
request. This is useful for debugging slow endpoints during
development.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``install_database_connection``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
By default, Galaxy will use the same database to track user data
and tool shed install data. There are many situations in which it
is valuable to separate these - for instance bootstrapping fresh
Galaxy instances with pretested installs. The following option
can be used to separate the tool shed install database (all other
options listed above but prefixed with ``install_`` are also
available).
Defaults to the value of the 'database_connection' option.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``database_auto_migrate``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Setting the following option to true will cause Galaxy to
automatically migrate the database forward after updates. This is
not recommended for production use.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~
``database_wait``
~~~~~~~~~~~~~~~~~
:Description:
Wait for database to become available instead of failing
immediately.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_wait_attempts``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Number of attempts before failing if database_wait is enabled.
:Default: ``60``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~
``database_wait_sleep``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time to sleep between attempts if database_wait is enabled (in
seconds).
:Default: ``1.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``history_audit_table_prune_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time (in seconds) between attempts to remove old rows from the
history_audit database table. Set to 0 to disable pruning.
:Default: ``3600``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``kombu_sqla_transport_cleanup_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time (in seconds) between attempts to delete fully-consumed rows
from the Kombu SQLAlchemy transport tables (``kombu_message``).
Only relevant when ``amqp_internal_connection`` uses a
``sqlalchemy+*`` scheme (the default with an on-disk
control.sqlite); the SQLAlchemy transport has no built-in TTL, so
without this task the tables grow unbounded. The task no-ops on
non-SQLAlchemy brokers (RabbitMQ/Redis honor per-message
expiration natively). Set to 0 to disable the cleanup task.
:Default: ``900``
:Type: int
~~~~~~~~~~~~~
``file_path``
~~~~~~~~~~~~~
:Description:
Where dataset files are stored. It must be accessible at the same
path on any cluster nodes that will run Galaxy jobs, unless using
Pulsar. The default value has been changed from 'files' to
'objects' as of 20.05; however, Galaxy will first check if the
'files' directory exists before using 'objects' as the default.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``objects``
:Type: str
~~~~~~~~~~~~~~~~~
``new_file_path``
~~~~~~~~~~~~~~~~~
:Description:
Where temporary files are stored. It must be accessible at the
same path on any cluster nodes that will run Galaxy jobs, unless
using Pulsar.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``tmp``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``maximum_upload_file_size``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Maximum size of uploadable files, specified in bytes (default:
100GB). This value is ignored if an external upload server is
configured.
:Default: ``107374182400``
:Type: int
~~~~~~~~~~~~~~~~~~~~
``tool_config_file``
~~~~~~~~~~~~~~~~~~~~
:Description:
Tool config files, defines what tools are available in Galaxy.
Tools can be locally developed or installed from Galaxy tool
sheds. (config/tool_conf.xml.sample will be used if left unset and
config/tool_conf.xml does not exist). Can be a single file, a list
of files, or (for backwards compatibility) a comma-separated list
of files.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_conf.xml``
:Type: any
~~~~~~~~~~~~~~~~~~~~~~~~~
``shed_tool_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Tool config file for tools installed from the Galaxy Tool Shed.
Must be writable by Galaxy and generally should not be edited by
hand. In older Galaxy releases, this file was part of the
tool_config_file option. It is still possible to specify this file
(and other shed-enabled tool config files) in tool_config_file,
but in the standard case of a single shed-enabled tool config,
this option is preferable. This file will be created automatically
upon tool installation, whereas Galaxy will fail to start if any
files in tool_config_file cannot be read.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``shed_tool_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``migrated_tools_config``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This option is deprecated. In previous releases this file was
maintained by tool migration scripts that are no longer part of
the code base. The option remains as a placeholder for deployments
where these scripts were previously run and such a file exists.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``migrated_tools_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``integrated_tool_panel_config``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
File that contains the XML section and tool tags from all tool
panel config files integrated into a single file that defines the
tool panel layout. This file can be changed by the Galaxy
administrator to alter the layout of the tool panel. If not
present, Galaxy will create it.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``integrated_tool_panel.xml``
:Type: str
~~~~~~~~~~~~~
``tool_path``
~~~~~~~~~~~~~
:Description:
Default path to the directory containing the tools defined in
tool_conf.xml. Other tool config files must include the tool_path
as an attribute in the <toolbox> tag.
:Default: ``tools``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_source_database_connection``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
SQLAlchemy connection string for storing pre-parsed tool sources.
The store is a rebuildable cache that lives outside Galaxy's
database. This URI is used by tool source storage code paths,
including the population script and lazy toolbox consumers.
Runtime use also requires a populated store and a toolbox consumer
configured to read from tool source storage.
By default, Galaxy uses a SQLite database at
``<data_dir>/tool_sources.sqlite``. Multi-host deployments should
point every process at the same SQLAlchemy URI, such as a SQLite
file on a shared filesystem or a shared PostgreSQL database.
Sample default ``sqlite:///<data_dir>/tool_sources.sqlite``.
To populate the store, run: python
scripts/tool_source/populate_store.py
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``tool_source_stores``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Optional named tool source stores referenced from individual
tool_conf files via a top-level ``store="<name>"`` attribute (XML)
or ``store: <name>`` key (YAML). When any tool_conf opts in, the
process composes its named store with the default
(``tool_source_database_connection``) store at runtime, with reads
tried in declared order and writes always landing on the default.
Each entry takes a SQLAlchemy ``url`` and an optional ``read_only:
true`` flag. For SQLite connection-level read-only, use a SQLite
URI with ``mode=ro&uri=true``.
An entry may also declare a freshness probe via ``freshness``. The
populator stamps the probe's value into the store's persisted
index; at boot a matching value proves the store still covers the
tool tree and skips the per-tool coverage scan entirely.
``freshness: cvmfs`` reads the CernVM-FS repository revision (one
extended-attribute syscall) from ``freshness_path``, defaulting to
the store's SQLite file location — the right probe for a store
published on CVMFS in the same transaction as the tools it
indexes. ``freshness: tool_confs`` hashes the local tool conf
files plus tool_dir directory mtimes; the default
(``tool_source_database_connection``) store always uses this
probe. Without ``freshness``, a named store is verified by the
coverage scan as before.
:Default: ``None``
:Type: map
~~~~~~~~~~~~~~~~~~~~
``use_lazy_toolbox``
~~~~~~~~~~~~~~~~~~~~
:Description:
When true, use the LazyToolBox which loads tools on demand from
the tool source store. Otherwise (the default), the traditional
eager ToolBox is used and any per-conf ``store="..."`` attributes
on tool_conf files are ignored. Opt-in is explicit: a populated
tool source store does not flip a default deployment to lazy mode.
:Default: ``None``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``lazy_toolbox_cache_size``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Maximum number of fully constructed Tool objects the LazyToolBox
keeps in its in-memory LRU cache. Larger values reduce repeat
parsing cost for popular tools at the expense of memory.
:Default: ``500``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``watch_tool_source_stores``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Poll the freshness probes of read-only tool source stores and
reload the lazy toolbox index when a store's token changes (for
example, a new CVMFS repository revision was published).
Filesystem event watchers do not fire on CVMFS, so polling is the
only reliable signal; each poll costs one extended-attribute read
per watched store. Only meaningful with ``use_lazy_toolbox`` and a
``tool_source_stores`` entry declaring a freshness probe. The
admin toolbox-reload API remains available as a manual trigger.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_source_store_watch_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Seconds between freshness polls when ``watch_tool_source_stores``
is enabled. CVMFS clients only refresh their catalogs every few
minutes, so sub-minute polling buys nothing.
:Default: ``60.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~
``tool_dependency_dir``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Various dependency resolver configuration parameters will have
defaults set relative to this path, such as the default conda
prefix, default Galaxy packages path, legacy tool shed
dependencies path, and the dependency cache directory.
Set the string to null to explicitly disable tool dependency
handling. If this option is set to none or an invalid path,
installing tools with dependencies from the Tool Shed or in Conda
will fail.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``dependencies``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dependency_resolvers_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Specifies the path to the standalone dependency resolvers
configuration file. This configuration can now be specified
directly in the Galaxy configuration, see the description of the
'dependency_resolvers' option for details.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``dependency_resolvers_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~
``conda_prefix``
~~~~~~~~~~~~~~~~
:Description:
conda_prefix is the location on the filesystem where Conda
packages and environments are installed.
Sample default '<tool_dependency_dir>/_conda'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~
``conda_exec``
~~~~~~~~~~~~~~
:Description:
Override the Conda executable to use, it will default to the one
on the PATH (if available) and then to <conda_prefix>/bin/conda
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~
``conda_debug``
~~~~~~~~~~~~~~~
:Description:
Pass debug flag to conda commands.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~
``conda_ensure_channels``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
conda channels to enable by default
(https://conda.io/docs/user-guide/tasks/manage-channels.html)
:Default: ``conda-forge,bioconda``
:Type: str
~~~~~~~~~~~~~~~~~~~
``conda_use_local``
~~~~~~~~~~~~~~~~~~~
:Description:
Use locally-built conda packages.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~
``conda_auto_install``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set to true to instruct Galaxy to look for and install missing
tool dependencies before each job runs.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~
``conda_auto_init``
~~~~~~~~~~~~~~~~~~~
:Description:
Set to true to instruct Galaxy to install Conda from the web
automatically if it cannot find a local copy and conda_exec is not
configured. The default is true if running Galaxy from source, and
false if running from installed packages.
:Default: ``None``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``conda_copy_dependencies``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
You must set this to true if conda_prefix and
job_working_directory are not on the same volume, or some conda
dependencies will fail to execute at job runtime. Conda will copy
packages content instead of creating hardlinks or symlinks. This
will prevent problems with some specific packages (perl, R), at
the cost of extra disk space usage and extra time spent copying
packages.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``local_conda_mapping_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to a file that provides a mapping from abstract packages to
concrete conda packages. See
`config/local_conda_mapping.yml.sample` for examples.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``local_conda_mapping.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``modules_mapping_files``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to a file that provides a mapping from abstract packages to
locally installed modules. See
`config/environment_modules_mapping.yml.sample` for examples.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``environment_modules_mapping.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``use_cached_dependency_manager``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Certain dependency resolvers (namely Conda) take a considerable
amount of time to build an isolated job environment in the
job_working_directory if the job working directory is on a network
share. Set this option to true to cache the dependencies in a
folder. This option is beta and should only be used if you
experience long waiting times before a job is actually submitted
to your cluster.
This only affects tools where some requirements can be resolved
but not others, most modern best practice tools can use prebuilt
environments in the Conda directory.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_dependency_cache_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
By default the tool_dependency_cache_dir is the _cache directory
of the tool dependency directory.
Sample default '<tool_dependency_dir>/_cache'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``precache_dependencies``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
By default, when using a cached dependency manager, the
dependencies are cached when installing new tools and when using
tools for the first time. Set this to false if you prefer
dependencies to be cached only when installing new tools.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_sheds_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
File containing the Galaxy Tool Sheds that should be made
available to install from in the admin interface (.sample used if
default does not exist).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_sheds_conf.xml``
:Type: str
~~~~~~~~~~~~~~~
``watch_tools``
~~~~~~~~~~~~~~~
:Description:
Monitor the tools and tool directories listed in any tool config
file specified in tool_config_file option. If changes are found,
tools are automatically reloaded. Watchdog (
https://pypi.org/project/watchdog/ ) must be installed and
available to Galaxy to use this option. Other options include
'auto' which will attempt to watch tools if the watchdog library
is available but won't fail to load Galaxy if it is not and
'polling' which will use a less efficient monitoring scheme that
may work in wider range of scenarios than the watchdog default.
:Default: ``false``
:Type: str
~~~~~~~~~~~~~~~~~~~
``watch_job_rules``
~~~~~~~~~~~~~~~~~~~
:Description:
Monitor dynamic job rules. If changes are found, rules are
automatically reloaded. Takes the same values as the 'watch_tools'
option.
:Default: ``false``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``watch_core_config``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Monitor a subset of options in the core configuration file (See
RELOADABLE_CONFIG_OPTIONS in lib/galaxy/config/__init__.py). If
changes are found, modified options are automatically reloaded.
Takes the same values as the 'watch_tools' option.
:Default: ``false``
:Type: str
~~~~~~~~~~~~~~~
``watch_tours``
~~~~~~~~~~~~~~~
:Description:
Monitor the interactive tours directory specified in the
'tour_config_dir' option. If changes are found, modified tours are
automatically reloaded. Takes the same values as the 'watch_tools'
option.
:Default: ``false``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~
``short_term_storage_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Location of files available for a short time as downloads (short
term storage). This directory is exclusively used for serving
dynamically generated downloadable content. Galaxy may use the
new_file_path parameter as a general temporary directory and that
directory should be monitored by a tool such as tmpwatch in
production environments. short_term_storage_dir on the other hand
is monitored by Galaxy's task framework and should not require
such external tooling.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``short_term_web_storage``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``short_term_storage_default_duration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Default duration before short term web storage files will be
cleaned up by Galaxy tasks (in seconds). The default duration is 1
day.
:Default: ``86400``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``short_term_storage_maximum_duration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The maximum duration short term storage files can hosted before
they will be marked for clean up. The default setting of 0
indicates no limit here.
:Default: ``0``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``short_term_storage_cleanup_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
How many seconds between instances of short term storage being
cleaned up in default Celery task configuration.
:Default: ``3600``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``bulk_storage_operation_dataset_minimum_days_to_expiration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Minimum remaining lifetime, in days, required before a dataset can
be moved into an object store with automatic expiration. This
prevents moving data into a target store where it would be close
to expiring immediately. Defaults to 7 days.
:Default: ``7``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``bulk_storage_operation_completed_run_retention_days``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
How long completed bulk dataset storage operation runs are kept in
the database before Galaxy prunes their run records. Snapshot
cleanup is handled separately. Defaults to 30 days.
:Default: ``30``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``prune_expired_bulk_storage_operations_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
How many seconds between attempts to prune expired bulk dataset
storage operation snapshots and old completed run records. Set to
0 to disable the periodic pruning task. Defaults to every 24
hours.
:Default: ``86400``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``recover_stale_bulk_storage_operation_runs_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
How many seconds between attempts to recover bulk dataset storage
operation runs that were left pending or running after a worker
stopped updating them. Defaults to every hour.
:Default: ``3600``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``file_sources_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configured FileSource plugins.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``file_sources_conf.yml``
:Type: str
~~~~~~~~~~~~~~~~
``file_sources``
~~~~~~~~~~~~~~~~
:Description:
FileSource plugins described embedded into Galaxy's config.
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_templates_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configured Object Store templates configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``object_store_templates.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_templates``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configured Object Store templates embedded into Galaxy's config.
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_templates_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configured user file source templates configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``file_source_templates.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_templates``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configured user file source templates embedded into Galaxy's
config.
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_config_templates_use_saved_configuration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
User defined object stores and file sources are saved in the
database with their last valid configuration. It may be the case
that the admin changes file source and object store templates over
time such that the variables and secrets an instance is saved with
no longer match the configuration's expected values. For this
reason, admins should always add new versions of templates instead
of just changing them - however people take shortcuts and
divergences might happen. If a template is changed in such a way
it breaks or if a template disappears from the library of
templates this parameter controls how and if the database version
will be used.
By default, it will simply be used as a 'fallback' if a
configuration cannot be resolved against the template version in
the configuration file. Using 'preferred' instead will mean the
stored database version is always used. This ensures a greater
degree of reproducibility without effort on the part of the admin
but also means that small issues are not easy to fix. Using
'never' instead will ensure the config templates are always only
loaded from the template library files - this might make sense for
admins who want to disable templates without worrying about the
contents of the database.
:Default: ``fallback``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_mulled_containers``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable Galaxy to fetch containers registered with quay.io
generated from tool requirements resolved through Conda. These
containers (when available) have been generated using mulled -
https://github.com/mulled. Container availability will vary by
tool, this option will only be used for job destinations with
Docker or Singularity enabled.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``container_resolvers_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Container resolvers configuration. Set up a file describing
container resolvers to use when discovering containers for Galaxy.
If this is set to None, the default container resolvers loaded is
determined by enable_mulled_containers. For available options see
https://docs.galaxyproject.org/en/master/admin/container_resolvers.html
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``container_resolvers``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Rather than specifying a container_resolvers_config_file, the
definition of the resolvers to enable can be embedded into
Galaxy's config with this option. This has no effect if a
container_resolvers_config_file is used. Takes the same options
that can be set in container_resolvers_config_file.
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~
``involucro_path``
~~~~~~~~~~~~~~~~~~
:Description:
involucro is a tool used to build Docker or Singularity containers
for tools from Conda dependencies referenced in tools as
`requirement` s. The following path is the location of involucro
on the Galaxy host. This is ignored if the relevant container
resolver isn't enabled, and will install on demand unless
involucro_auto_init is set to false.
The value of this option will be resolved with respect to
<tool_dependency_dir>.
:Default: ``involucro``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``involucro_auto_init``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Install involucro as needed to build Docker or Singularity
containers for tools. Ignored if relevant container resolver is
not used.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~
``mulled_channels``
~~~~~~~~~~~~~~~~~~~
:Description:
Conda channels to use when building Docker or Singularity
containers using involucro.
:Default: ``conda-forge,bioconda``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_tool_shed_check``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable automatic polling of relative tool sheds to see if any
updates are available for installed repositories. Ideally only
one Galaxy server process should be able to check for repository
updates. The setting for hours_between_check should be an integer
between 1 and 24.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~
``hours_between_check``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable automatic polling of relative tool sheds to see if any
updates are available for installed repositories. Ideally only
one Galaxy server process should be able to check for repository
updates. The setting for hours_between_check should be an integer
between 1 and 24.
:Default: ``12``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_data_table_config_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
XML config file that contains data table entries for the
ToolDataTableManager. This file is manually maintained by the
Galaxy administrator (.sample used if default does not exist).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_data_table_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``shed_tool_data_table_config``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
XML config file that contains additional data table entries for
the ToolDataTableManager. This file is automatically generated
based on the current installed tool shed repositories that contain
valid tool_data_table_conf.xml.sample files. At the time of
installation, these entries are automatically added to the
following file, which is parsed and applied to the
ToolDataTableManager at server start up.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``shed_tool_data_table_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~
``tool_data_path``
~~~~~~~~~~~~~~~~~~
:Description:
Directory where data used by tools is located. See the samples in
that directory and the Galaxy Community Hub for help:
https://galaxyproject.org/admin/data-integration
:Default: ``tool-data``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``shed_tool_data_path``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Directory where Tool Data Table related files will be placed when
installed from a ToolShed. Defaults to the value of the
'tool_data_path' option.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``watch_tool_data_dir``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Monitor the tool_data and shed_tool_data_path directories. If
changes in tool data table files are found, the tool data tables
for that data manager are automatically reloaded. Watchdog (
https://pypi.org/project/watchdog/ ) must be installed and
available to Galaxy to use this option. Other options include
'auto' which will attempt to use the watchdog library if it is
available but won't fail to load Galaxy if it is not and 'polling'
which will use a less efficient monitoring scheme that may work in
wider range of scenarios than the watchdog default.
:Default: ``false``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``refgenie_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
File containing refgenie configuration, e.g.
/path/to/genome_config.yaml. Can be used by refgenie backed tool
data tables.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``build_sites_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
File that defines the builds (dbkeys) available at sites used by
display applications and the URL to those sites.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``build_sites.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``builds_file_path``
~~~~~~~~~~~~~~~~~~~~
:Description:
File containing old-style genome builds.
The value of this option will be resolved with respect to
<tool_data_path>.
:Default: ``shared/ucsc/builds.txt``
:Type: str
~~~~~~~~~~~~~~~~~
``len_file_path``
~~~~~~~~~~~~~~~~~
:Description:
Directory where chrom len files are kept.
The value of this option will be resolved with respect to
<tool_data_path>.
:Default: ``shared/ucsc/chrom``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``datatypes_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Datatypes config file(s), defines what data (file) types are
available in Galaxy (.sample is used if default does not exist).
If a datatype appears in multiple files, the last definition is
used (though the first sniffer is used so limit sniffer
definitions to one file).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``datatypes_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``sniff_compressed_dynamic_datatypes_default``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable sniffing of compressed datatypes. This can be
configured/overridden on a per-datatype basis in the
datatypes_conf.xml file. With this option set to false the
compressed datatypes will be unpacked before sniffing.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``datatypes_disable_auto``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Disable the 'Auto-detect' option for file uploads
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``visualization_plugins_directory``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Visualizations config directory: where to look for individual
visualization plugins. The path is relative to the Galaxy root
dir. To use an absolute path begin the path with '/'. This is a
comma-separated list.
:Default: ``config/plugins/visualizations``
:Type: str
~~~~~~~~~~~~~~~~~~~
``tour_config_dir``
~~~~~~~~~~~~~~~~~~~
:Description:
Interactive tour directory: where to store interactive tour
definition files. Galaxy ships with several basic interface tours
enabled, though a different directory with custom tours can be
specified here. The path is relative to the Galaxy root dir. To
use an absolute path begin the path with '/'. This is a
comma-separated list.
:Default: ``config/plugins/tours``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_tool_generated_tours``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow tools to show the option of and create interactive tours
crafted for them by the backend.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~
``webhooks_dir``
~~~~~~~~~~~~~~~~
:Description:
Webhooks directory: where to store webhooks - plugins to extend
the Galaxy UI. By default none will be loaded. Set to
config/plugins/webhooks/demo to load Galaxy's demo webhooks. To
use an absolute path begin the path with '/'. This is a
comma-separated list. Add test/functional/webhooks to this list to
include the demo webhooks used to test the webhook framework.
:Default: ``config/plugins/webhooks``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``job_working_directory``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Each job is given a unique empty directory as its current working
directory. This option defines in what parent directory those
directories will be created.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``jobs_directory``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``template_cache_path``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Mako templates are compiled as needed and cached for reuse, this
directory is used for the cache
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``compiled_templates``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``check_job_script_integrity``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set to false to disable various checks Galaxy will do to ensure it
can run job scripts before attempting to execute or submit them.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``check_job_script_integrity_count``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Number of checks to execute if check_job_script_integrity is
enabled.
:Default: ``35``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``check_job_script_integrity_sleep``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time to sleep between checks if check_job_script_integrity is
enabled (in seconds).
:Default: ``0.25``
:Type: float
~~~~~~~~~~~~~~~~~~~~~
``default_job_shell``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the default shell used by non-containerized jobs Galaxy-wide.
This defaults to bash for all jobs and can be overridden at the
destination level for heterogeneous clusters. conda job resolution
requires bash or zsh so if this is switched to /bin/sh for
instance - conda resolution should be disabled. Containerized jobs
always use /bin/sh - so for maximum portability tool authors
should assume generated commands run in sh.
:Default: ``/bin/bash``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_search_index_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Directory in which the toolbox search index is stored. The value
of this option will be resolved with respect to <data_dir>.
:Default: ``tool_search_index``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_tag_mappings_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Optional YAML file mapping tool ids to curated tag names. Tags
drive the `tag:` autocompletion, the favorite-tags grouping in the
My Tools panel, and the `tool_tags` Whoosh search field. If unset,
Galaxy ships a small example covering the tools used by its own
integration tests; admins who want production-grade tag coverage
can generate a snapshot for their instance with
`scripts/extract_tool_sections_from_api.py`. The file must be a
YAML document with a top-level `tool_tags:` mapping from tool id
to a list of tag names.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``biotools_content_directory``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Point Galaxy at a repository consisting of a copy of the bio.tools
database (e.g. https://github.com/bio-tools/content/) to resolve
bio.tools data for tool metadata.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``biotools_use_api``
~~~~~~~~~~~~~~~~~~~~
:Description:
Set this to true to attempt to resolve bio.tools metadata for
tools for tool not resolved via biotools_content_directory.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``biotools_service_cache_type``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
bio.tools web service request related caching. The type of beaker
cache used.
:Default: ``file``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``biotools_service_cache_data_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
bio.tools web service request related caching. The data directory
to point beaker cache at.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``biotools/data``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``biotools_service_cache_lock_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
bio.tools web service request related caching. The lock directory
to point beaker cache at.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``biotools/locks``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``biotools_service_cache_url``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When biotools_service_cache_type = ext:database, this is the url
of the database used by beaker for bio.tools web service request
related caching. The application config code will set it to the
value of database_connection if this is not set.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``biotools_service_cache_table_name``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When biotools_service_cache_type = ext:database, this is the
database table name used by beaker for bio.tools web service
request related caching.
:Default: ``beaker_cache``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``biotools_service_cache_schema_name``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When biotools_service_cache_type = ext:database, this is the
database table name used by beaker for bio.tools web service
request related caching.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``citation_cache_type``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Citation related caching. Tool citations information maybe
fetched from external sources such as https://doi.org/ by Galaxy -
the following parameters can be used to control the caching used
to store this information.
:Default: ``file``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``citation_cache_data_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Citation related caching. Tool citations information maybe
fetched from external sources such as https://doi.org/ by Galaxy -
the following parameters can be used to control the caching used
to store this information.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``citations/data``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``citation_cache_lock_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Citation related caching. Tool citations information maybe
fetched from external sources such as https://doi.org/ by Galaxy -
the following parameters can be used to control the caching used
to store this information.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``citations/locks``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``citation_cache_url``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
When citation_cache_type = ext:database, this is the url of the
database used by beaker for citation caching. The application
config code will set it to the value of database_connection if
this is not set.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``citation_cache_table_name``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When citation_cache_type = ext:database, this is the database
table name used by beaker for citation related caching.
:Default: ``beaker_cache``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``citation_cache_schema_name``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When citation_cache_type = ext:database, this is the database
schema name of the table used by beaker for citation related
caching.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``mulled_resolution_cache_type``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Mulled resolution caching. Mulled resolution uses external APIs of
quay.io, these requests are caching using this and the following
parameters
:Default: ``file``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``mulled_resolution_cache_data_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Data directory used by beaker for caching mulled resolution
requests.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``mulled/data``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``mulled_resolution_cache_lock_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Lock directory used by beaker for caching mulled resolution
requests.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``mulled/locks``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``mulled_resolution_cache_expire``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Seconds until the beaker cache is considered old and a new value
is created.
:Default: ``3600``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``mulled_resolution_cache_url``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When mulled_resolution_cache_type = ext:database, this is the url
of the database used by beaker for caching mulled resolution
requests. The application config code will set it to the value of
database_connection if this is not set.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``mulled_resolution_cache_table_name``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When mulled_resolution_cache_type = ext:database, this is the
database table name used by beaker for caching mulled resolution
requests.
:Default: ``beaker_cache``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``mulled_resolution_cache_schema_name``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When mulled_resolution_cache_type = ext:database, this is the
database schema name of the table used by beaker for caching
mulled resolution requests.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configuration file for the object store If this is set and exists,
it overrides any other objectstore settings.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``object_store_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``object_store_config``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Rather than specifying an object_store_config_file, the object
store configuration can be embedded into Galaxy's config with this
option.
This option has no effect if the file specified by
object_store_config_file exists. Otherwise, if this option is set,
it overrides any other objectstore settings.
The syntax, available storage plugins, and documentation of their
options is explained in detail in the object store sample
configuration file, `object_store_conf.sample.yml`
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_cache_monitor_driver``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Specify where cache monitoring is driven for caching object stores
such as S3, Azure, and iRODS. This option has no affect on disk
object stores. For production instances, the cache should be
monitored by external tools such as tmpwatch and this value should
be set to 'external'. This will disable all cache monitoring in
Galaxy. Alternatively, 'celery' can monitor caches using a
periodic task or an 'inprocess' thread can be used - but this last
option seriously limits Galaxy's ability to scale. The default of
'auto' will use 'celery' if 'enable_celery_tasks' is set to true
or 'inprocess' otherwise. This option serves as the default for
all object stores and can be overridden on a per object store
basis (but don't - just setup tmpwatch for all relevant cache
paths).
:Default: ``auto``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_cache_monitor_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
For object store cache monitoring done by Galaxy, this is the
interval between cache checking steps. This is used by both
inprocess cache monitors (which we recommend you do not use) and
by the celery task if it is configured (by setting
enable_celery_tasks to true and not setting
object_store_cache_monitor_driver to external).
:Default: ``600``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_cache_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Default cache path for caching object stores if cache not
configured for that object store entry.
The value of this option will be resolved with respect to
<cache_dir>.
:Default: ``object_store_cache``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_cache_size``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Default cache size, in GB, for caching object stores if the cache
is not configured for that object store entry.
:Default: ``-1``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_always_respect_user_selection``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set this to true to indicate in the UI that a user's object store
selection isn't simply a "preference" that job destinations often
respect but in fact will always be respected. This should be set
to true to simplify the UI as long as job destinations never
override 'object_store_id's for a jobs.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~
``object_store_store_by``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
What Dataset attribute is used to reference files in an
ObjectStore implementation, this can be 'uuid' or 'id'. The
default will depend on how the object store is configured,
starting with 20.05 Galaxy will try to default to 'uuid' if it can
be sure this is a new Galaxy instance - but the default will be
'id' in many cases. In particular, if the name of the directory
set in <file_path> is `objects`, the default will be set to
'uuid', otherwise it will be 'id'.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~
``smtp_server``
~~~~~~~~~~~~~~~
:Description:
Galaxy sends mail for various things: subscribing users to the
mailing list if they request it, password resets, reporting
dataset errors, and sending activation emails. To do this, it
needs to send mail through an SMTP server, which you may define
here (host:port). Galaxy will automatically try STARTTLS but will
continue upon failure.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~
``smtp_username``
~~~~~~~~~~~~~~~~~
:Description:
If your SMTP server requires a username and password, you can
provide them here (password in cleartext here, but if your server
supports STARTTLS it will be sent over the network encrypted).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~
``smtp_password``
~~~~~~~~~~~~~~~~~
:Description:
If your SMTP server requires a username and password, you can
provide them here (password in cleartext here, but if your server
supports STARTTLS it will be sent over the network encrypted).
:Default: ``None``
:Type: str
~~~~~~~~~~~~
``smtp_ssl``
~~~~~~~~~~~~
:Description:
If your SMTP server requires SSL from the beginning of the
connection
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``mailing_join_addr``
~~~~~~~~~~~~~~~~~~~~~
:Description:
On the user registration form, users may choose to join a mailing
list. This is the address used to subscribe to the list. Uncomment
and leave empty if you want to remove this option from the user
registration form.
Example value 'galaxy-announce-join@lists.galaxyproject.org'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``mailing_join_subject``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The subject of the email sent to the mailing list join address.
See the `mailing_join_addr` option for more information.
:Default: ``Join Mailing List``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``mailing_join_body``
~~~~~~~~~~~~~~~~~~~~~
:Description:
The body of the email sent to the mailing list join address. See
the `mailing_join_addr` option for more information.
:Default: ``Join Mailing List``
:Type: str
~~~~~~~~~~~~~~~~~~
``error_email_to``
~~~~~~~~~~~~~~~~~~
:Description:
Datasets in an error state include a link to report the error.
Those reports will be sent to this address. Error reports are
disabled if no address is set. Also this email is shown as a
contact to user in case of Galaxy misconfiguration and other
events user may encounter.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~
``email_from``
~~~~~~~~~~~~~~
:Description:
Email address to use in the 'From' field when sending emails for
account activations, workflow step notifications, password resets,
and tool error reports. We recommend using a string in the
following format: Galaxy Project <galaxy-no-reply@example.com>. If
not configured, '<galaxy-no-reply@HOSTNAME>' will be used.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``custom_activation_email_message``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This text will be inserted at the end of the activation email's
message, before the 'Your Galaxy Team' signature.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``instance_resource_url``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
URL of the support resource for the galaxy instance. Used outside
of web contexts such as in activation emails and in Galaxy
markdown report generation.
Example value 'https://galaxyproject.org/'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``instance_access_url``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
URL used to access this Galaxy server. Used outside of web
contexts such as in Galaxy markdown report generation.
Example value 'https://usegalaxy.org'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``email_domain_blocklist_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
E-mail domains blocklist is used for filtering out users that are
using disposable email addresses at registration. If their
address's base domain matches any domain on the list, they are
refused registration. Address subdomains are ignored (both
'name@spam.com' and 'name@foo.spam.com' will match 'spam.com').
Example value 'email_blocklist.conf'
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``email_domain_allowlist_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
E-mail domains allowlist is used to specify allowed email address
domains. If the list is non-empty and a user attempts registration
using an email address belonging to a domain that is not on the
list, registration will be denied. Unlike
<email_domain_allowlist_file> which matches the address's base
domain, here email addresses are matched against the full domain
(base + subdomain). This is a more restrictive option than
<email_domain_blocklist_file>, and therefore, in case
<email_domain_allowlist_file> is set and is not empty,
<email_domain_blocklist_file> will be ignored.
Example value 'email_allowlist.conf'
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~
``email_ban_file``
~~~~~~~~~~~~~~~~~~
:Description:
E-mail ban file is used to specify email addresses that have been
banned. If a user attempts to register a new account using an
email address listed in this file, registration will be denied.
This file does not affect user sign-in. Email addresses are
matched against a canonical address representation based on rules
defined in <canonical_email_rules>. The file should include one
email address per line. Lines starting with the "#" character are
ignored.
Example value "banned_emails.conf"
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``canonical_email_rules``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Specifies how email addresses are reduced to their canonical form
by assigning rules to email service domains and domain aliases.
Available rules - ignore_case Values are not case-sensitive
(RickDeckard@foo.cOM == rickdeckard@foo.com) - ignore_dots
Periods in the local-part of an email address are ignored
(rick.deckard@foo.com == rickdeckard@foo.com) - sub_addressing
Suffixes prefixed with <sub_addressing_delim> in the local-part of
an email address are ignored (rickdeckard+anything@foo.com ==
rickdeckard@foo.com if delimiter is the character '+')
:Default: ``{'all': {'ignore_case': False, 'ignore_dots': False, 'sub_addressing': False, 'sub_addressing_delim': '+'}, 'gmail.com': {'aliases': ['googlemail.com'], 'ignore_case': True, 'ignore_dots': True, 'sub_addressing': True}, 'proton.me': {'aliases': ['pm.me', 'protonmail.com'], 'ignore_case': True, 'sub_addressing': True}}``
:Type: map
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``registration_warning_message``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Registration warning message is used to discourage people from
registering multiple accounts. Applies mostly for the main Galaxy
instance. If no message specified the warning box will not be
shown.
:Default: ``Please register only one account to ensure fair sharing of computational resources. Multiple registrations are monitored and will result in account termination and data deletion.``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``user_activation_on``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
User account activation feature global flag. If set to false, the
rest of the Account activation configuration is ignored and user
activation is disabled (i.e. accounts are active since
registration). The activation is also not working in case the SMTP
server is not defined.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``activation_grace_period``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Activation grace period (in hours). Activation is not forced
(login is not disabled) until grace period has passed. Users
under grace period can't run jobs. Enter 0 to disable grace
period.
:Default: ``3``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~
``inactivity_box_content``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Shown in warning box to users that were not activated yet. In use
only if activation_grace_period is set.
:Default: ``Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address.``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``password_expiration_period``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Password expiration period (in days). Users are required to change
their password every x days. Users will be redirected to the
change password screen when they log in after their password
expires. Enter 0 to disable password expiration.
:Default: ``0``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_account_interface``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow users to manage their account data, change passwords or
delete their accounts.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~
``session_duration``
~~~~~~~~~~~~~~~~~~~~
:Description:
Galaxy Session Timeout This provides a timeout (in minutes) after
which a user will have to log back in. A duration of 0 disables
this feature.
:Default: ``0``
:Type: int
~~~~~~~~~~~
``ga_code``
~~~~~~~~~~~
:Description:
You can enter tracking code here to track visitor's behavior
through your Google Analytics account. Example: UA-XXXXXXXX-Y
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``plausible_server``
~~~~~~~~~~~~~~~~~~~~
:Description:
Please enter the URL for the Plausible server (including https) so
this can be used for tracking with Plausible
(https://plausible.io/).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``plausible_domain``
~~~~~~~~~~~~~~~~~~~~
:Description:
Please enter the URL for the Galaxy server so this can be used for
tracking with Plausible (https://plausible.io/).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~
``matomo_server``
~~~~~~~~~~~~~~~~~
:Description:
Please enter the URL for the Matomo server (including https) so
this can be used for tracking with Matomo (https://matomo.org/).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~
``matomo_site_id``
~~~~~~~~~~~~~~~~~~
:Description:
Please enter the site ID for the Matomo server so this can be used
for tracking with Matomo (https://matomo.org/).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~
``display_servers``
~~~~~~~~~~~~~~~~~~~
:Description:
Galaxy can display data at various external browsers. These
options specify which browsers should be available. URLs and
builds available at these browsers are defined in the specified
files.
If use_remote_user is set to true, display application servers
will be denied access to Galaxy and so displaying datasets in
these sites will fail. display_servers contains a list of
hostnames which should be allowed to bypass security to display
datasets. Please be aware that there are security implications if
this is allowed. More details (including required changes to the
proxy server config) are available in the Apache proxy
documentation on the Galaxy Community Hub.
The list of servers in this sample config are for the UCSC Main,
Test and Archaea browsers, but the default if left commented is to
not allow any display sites to bypass security (you must uncomment
the line below to allow them).
:Default: ``hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_old_display_applications``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set this to false to disable the old-style display applications
that are hardcoded into datatype classes. This may be desirable
due to using the new-style, XML-defined, display applications that
have been defined for many of the datatypes that have the
old-style. There is also a potential security concern with the
old-style applications, where a malicious party could provide a
link that appears to reference the Galaxy server, but contains a
redirect to a third-party server, tricking a Galaxy user to access
said site.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~
``aws_estimate``
~~~~~~~~~~~~~~~~
:Description:
This flag enables an AWS cost estimate for every job based on
their runtime matrices. CPU, RAM and runtime usage is mapped
against AWS pricing table. Please note, that those numbers are
only estimates.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``carbon_emission_estimates``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This flag enables carbon emissions estimates for every job based
on its runtime metrics. CPU and RAM usage and the total job
runtime are used to determine an estimate value. These estimates
and are based off of the work of the Green Algorithms Project and
the United States Environmental Protection Agency (EPA). Visit
https://www.green-algorithms.org/ and
https://www.epa.gov/energy/greenhouse-gas-equivalencies-calculator.
for more detals.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``geographical_server_location_code``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The estimated geographical location of the server hosting your
galaxy instance given as an ISO 3166 code. This is used to make
carbon emissions estimates more accurate as the location effects
the carbon intensity values used in the estimate calculation. This
defaults to "GLOBAL" if not set or the
`geographical_server_location_code` value is invalid or
unsupported. To see a full list of supported locations, visit
https://docs.galaxyproject.org/en/master/admin/carbon_emissions.html
:Default: ``GLOBAL``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``power_usage_effectiveness``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The estimated power usage effectiveness of the data centre housing
the server your galaxy instance is running on. This can make
carbon emissions estimates more accurate. For more information on
how to calculate a PUE value, visit
https://en.wikipedia.org/wiki/Power_usage_effectiveness
:Default: ``1.67``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``interactivetools_enable``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable InteractiveTools.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``interactivetools_upstream_proxy``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set this to false to redirect users of Interactive tools directly
to the Interactive tools proxy. `interactivetools_upstream_proxy`
should only be set to false in development.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``interactivetools_proxy_host``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Hostname and port of Interactive tools proxy. It is assumed to be
hosted on the same hostname and port as Galaxy by default.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``interactivetools_base_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Base path for interactive tools running at a subpath without a
subdomain. Defaults to "/".
:Default: ``/``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``interactivetools_map``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Map for the interactivetool proxy. Mappings are stored in a SQLite
database file located on this path. As an alternative, you may
also store them in any other RDBMS supported by SQLAlchemy using
the option ``interactivetoolsproxy_map``, which overrides this
one.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``interactivetools_map.sqlite``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``interactivetoolsproxy_map``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Use a database supported by SQLAlchemy as map for the
interactivetool proxy. When this option is set, the value of
``interactivetools_map`` is ignored. The value of this option must
be a `SQLAlchemy database URL
<https://docs.sqlalchemy.org/en/20/core/engines.html#database-urls>`_.
Mappings are written to the table "gxitproxy" within the database.
This value cannot match ``database_connection`` nor
``install_database_connection``.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``interactivetools_prefix``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Prefix to use in the formation of the subdomain or path for
interactive tools
:Default: ``interactivetool``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``retry_interactivetool_metadata_internally``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Galaxy Interactive Tools (GxITs) can be stopped from within the
Galaxy interface, killing the GxIT job without completing its
metadata setting post-job steps. In such a case it may be
desirable to set metadata on job outputs internally (in the Galaxy
job handler process). The default is is the value of
`retry_metadata_internally`, which defaults to `true`.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``visualizations_visible``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Show visualization tab and list in masthead.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~
``message_box_visible``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Show a message box under the masthead.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~
``message_box_content``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Show a message box under the masthead.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``message_box_class``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Class of the message box under the masthead. Possible values are:
'info' (the default), 'warning', 'error', 'done'.
:Default: ``info``
:Type: str
~~~~~~~~~
``brand``
~~~~~~~~~
:Description:
Append "{brand}" text to the masthead.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``display_galaxy_brand``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This option has been deprecated, use the `logo_src` instead to
change the default logo including the galaxy brand title.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``pretty_datetime_format``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Format string used when showing date and time information. The
string may contain: - the directives used by Python
time.strftime() function (see
https://docs.python.org/library/time.html#time.strftime), -
$locale (complete format string for the server locale), - $iso8601
(complete format string as specified by ISO 8601 international
standard).
:Default: ``$locale (UTC)``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``trs_servers_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow import of workflows from the TRS servers configured in the
specified YAML or JSON file. The file should be a list with 'id',
'label', and 'api_url' for each entry. Optionally, 'link_url' and
'doc' may be specified as well for each entry.
If this is null (the default), a simple configuration containing
just Dockstore will be used.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``trs_servers_conf.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_preferences_extra_conf_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Location of the configuration file containing extra user
preferences.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``user_preferences_extra_conf.yml``
:Type: str
~~~~~~~~~~~~~~~~~~
``default_locale``
~~~~~~~~~~~~~~~~~~
:Description:
Default localization for Galaxy UI. Allowed values are listed at
the end of client/src/nls/locale.js. With the default value
(auto), the locale will be automatically adjusted to the user's
navigator language. Users can override this settings in their user
preferences if the localization settings are enabled in
user_preferences_extra_conf.yml
:Default: ``auto``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``galaxy_url_prefix``
~~~~~~~~~~~~~~~~~~~~~
:Description:
URL prefix for Galaxy application. If Galaxy should be served
under a prefix set this to the desired prefix value.
:Default: ``/``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``galaxy_infrastructure_url``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
URL (with schema http/https) of the Galaxy instance as accessible
within your local network. This URL is used as a default by pulsar
file staging and Interactive Tool containers for communicating
back with Galaxy via the API.
If you plan to run Interactive Tools make sure the docker
container can reach this URL.
:Default: ``http://localhost:8080``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``galaxy_infrastructure_web_port``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If the above URL cannot be determined ahead of time in dynamic
environments but the port which should be used to access Galaxy
can be - this should be set to prevent Galaxy from having to
guess. For example if Galaxy is sitting behind a proxy with
REMOTE_USER enabled - infrastructure shouldn't talk to Python
processes directly and this should be set to 80 or 443, etc... If
unset this file will be read for a server block defining a port
corresponding to the webapp.
:Default: ``8080``
:Type: int
~~~~~~~~~~~~~~~
``welcome_url``
~~~~~~~~~~~~~~~
:Description:
The URL of the page to display in Galaxy's middle pane when
loaded. This can be an absolute or relative URL.
:Default: ``/static/welcome.html``
:Type: str
~~~~~~~~~~~~
``logo_url``
~~~~~~~~~~~~
:Description:
The URL linked by the "Galaxy/brand" text.
:Default: ``/``
:Type: str
~~~~~~~~~~~~
``logo_src``
~~~~~~~~~~~~
:Description:
The brand image source.
:Default: ``/static/favicon.svg``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``logo_src_secondary``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
The custom brand image source.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~
``helpsite_url``
~~~~~~~~~~~~~~~~
:Description:
The URL linked by the "Galaxy Help" link in the "Help" menu.
:Default: ``https://help.galaxyproject.org/``
:Type: str
~~~~~~~~~~~~
``wiki_url``
~~~~~~~~~~~~
:Description:
The URL linked by the "Community Hub" link in the "Help" menu.
:Default: ``https://galaxyproject.org/``
:Type: str
~~~~~~~~~~~~~
``quota_url``
~~~~~~~~~~~~~
:Description:
The URL linked for quota information in the UI.
:Default: ``https://galaxyproject.org/support/account-quotas/``
:Type: str
~~~~~~~~~~~~~~~
``support_url``
~~~~~~~~~~~~~~~
:Description:
The URL linked by the "Support" link in the "Help" menu.
:Default: ``https://galaxyproject.org/support/``
:Type: str
~~~~~~~~~~~~~~~~
``citation_url``
~~~~~~~~~~~~~~~~
:Description:
The URL linked by the "How to Cite Galaxy" link in the "Help"
menu.
:Default: ``https://galaxyproject.org/citing-galaxy``
:Type: str
~~~~~~~~~~~~~~~~~~~
``citation_bibtex``
~~~~~~~~~~~~~~~~~~~
:Description:
The BibTeX citation for Galaxy, to be displayed in the History
Tool Reference List
:Default: ``@article{Galaxy2026, title="Galaxy for accessible, reproducible, and collaborative data analyses: 2026 update", author="{The Galaxy Community}", journal="Nucleic Acids Research", year="2026", doi="10.1093/nar/gkag469", url="https://doi.org/10.1093/nar/gkag469"}``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``release_doc_base_url``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The URL linked by the "Galaxy Version" link in the "Help" menu.
:Default: ``https://docs.galaxyproject.org/en/release_``
:Type: str
~~~~~~~~~~~~~~~~~~~
``screencasts_url``
~~~~~~~~~~~~~~~~~~~
:Description:
The URL linked by the "Videos" link in the "Help" menu.
:Default: ``https://www.youtube.com/c/galaxyproject``
:Type: str
~~~~~~~~~~~~~
``terms_url``
~~~~~~~~~~~~~
:Description:
The URL linked by the "Terms and Conditions" link in the "Help"
menu, as well as on the user registration and login forms and in
the activation emails.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~
``static_enabled``
~~~~~~~~~~~~~~~~~~
:Description:
Serve static content, which must be enabled if you're not serving
it via a proxy server. You can use these paths (or ones in the
proxy server) to point to your own styles. The static_* options
that refer to paths are relative to the current working directory.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``static_cache_time``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Value of cache time for static content served by Galaxy. Ignored
if static_enabled is false.
:Default: ``360``
:Type: int
~~~~~~~~~~~~~~
``static_dir``
~~~~~~~~~~~~~~
:Description:
Path to the static content dir. Ignored if static_enabled is
false.
:Default: ``static/``
:Type: str
~~~~~~~~~~~~~~~~~~~
``static_dist_dir``
~~~~~~~~~~~~~~~~~~~
:Description:
Path to the built Galaxy client application, static/dist/ in the
Galaxy source code after the build is complete. Ignored if
static_enabled is false.
:Default: ``static/dist/``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``static_images_dir``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to the static images directory. Ignored if static_enabled is
false.
:Default: ``static/images/``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``static_favicon_dir``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to favicon.ico, not the directory that contains it (the name
is a misnomer). Ignored if static_enabled is false.
:Default: ``static/favicon.ico``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``static_scripts_dir``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to the static scripts directory. Ignored if static_enabled is
false.
:Default: ``static/scripts/``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``static_style_dir``
~~~~~~~~~~~~~~~~~~~~
:Description:
Path to the static style directory. Ignored if static_enabled is
false.
:Default: ``static/style/``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``static_robots_txt``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to robots.txt. Ignored if static_enabled is false.
:Default: ``static/robots.txt``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``display_chunk_size``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Incremental Display Options
:Default: ``65536``
:Type: int
~~~~~~~~~~~~~~~~~~~~
``apache_xsendfile``
~~~~~~~~~~~~~~~~~~~~
:Description:
For help on configuring the Advanced proxy features, see:
https://docs.galaxyproject.org/en/master/admin/production.html
Apache can handle file downloads (Galaxy-to-user) via
mod_xsendfile. Set this to true to inform Galaxy that
mod_xsendfile is enabled upstream.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``nginx_x_accel_redirect_base``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The same download handling can be done by nginx using
X-Accel-Redirect. This should be set to the path defined in the
nginx config as an internal redirect with access to Galaxy's data
files (see documentation linked above).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~
``upstream_gzip``
~~~~~~~~~~~~~~~~~
:Description:
If using compression in the upstream proxy server, use this option
to disable gzipping of dataset collection and library archives,
since the upstream server will do it faster on the fly. To enable
compression add ``application/zip`` to the proxy's compressable
mimetypes.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~
``upstream_mod_zip``
~~~~~~~~~~~~~~~~~~~~
:Description:
If using the mod-zip module in nginx, use this option to assemble
zip archives in nginx. This is preferable over the upstream_gzip
option as Galaxy does not need to serve the archive. Requires
setting up internal nginx locations to all paths that can be
archived. See
https://docs.galaxyproject.org/en/master/admin/nginx.html#creating-archives-with-mod-zip
for details.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~
``x_frame_options``
~~~~~~~~~~~~~~~~~~~
:Description:
The following default adds a header to web request responses that
will cause modern web browsers to not allow Galaxy to be embedded
in the frames of web applications hosted at other hosts - this can
help prevent a class of attack called clickjacking
(https://www.owasp.org/index.php/Clickjacking). If you configure
a proxy in front of Galaxy - please ensure this header remains
intact to protect your users. Uncomment and leave empty to not
set the `X-Frame-Options` header.
:Default: ``SAMEORIGIN``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``nginx_upload_store``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
nginx can also handle file uploads (user-to-Galaxy) via
nginx_upload_module. Configuration for this is complex and
explained in detail in the documentation linked above. The upload
store is a temporary directory in which files uploaded by the
upload module will be placed.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``nginx_upload_path``
~~~~~~~~~~~~~~~~~~~~~
:Description:
This value overrides the action set on the file upload form, e.g.
the web path where the nginx_upload_module has been configured to
intercept upload requests.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``nginx_upload_job_files_store``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Galaxy can also use nginx_upload_module to receive files staged
out upon job completion by remote job runners (i.e. Pulsar) that
initiate staging operations on the remote end. See the Galaxy
nginx documentation for the corresponding nginx configuration.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``nginx_upload_job_files_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Galaxy can also use nginx_upload_module to receive files staged
out upon job completion by remote job runners (i.e. Pulsar) that
initiate staging operations on the remote end. See the Galaxy
nginx documentation for the corresponding nginx configuration.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``tus_upload_store``
~~~~~~~~~~~~~~~~~~~~
:Description:
The upload store is a temporary directory in which files uploaded
by the tus middleware or server for user uploads will be placed.
Defaults to new_file_path if not set.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tus_upload_store_job_files``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The upload store is a temporary directory in which files uploaded
by the tus middleware or server for remote job files (Pulsar) will
be placed. Defaults to tus_upload_store if not set.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``chunk_upload_size``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Galaxy can upload user files in chunks without using nginx. Enable
the chunk uploader by specifying a chunk size larger than 0. The
chunk size is specified in bytes (default: 10MB).
:Default: ``10485760``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_manage``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Have Galaxy manage dynamic proxy component for routing requests to
other services based on Galaxy's session cookie. It will attempt
to do this by default though you do need to install node+npm and
do an npm install from `lib/galaxy/web/proxy/js`. It is generally
more robust to configure this externally, managing it in the same
way Galaxy itself is managed. If true, Galaxy will only launch
the proxy if it is actually going to be used (e.g. for Jupyter).
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~
``dynamic_proxy``
~~~~~~~~~~~~~~~~~
:Description:
As of 16.04 Galaxy supports multiple proxy types. The original
NodeJS implementation, alongside a new Golang
single-binary-no-dependencies version. Valid values are (node,
golang)
:Default: ``node``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_session_map``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The NodeJS dynamic proxy can use an SQLite database or a JSON file
for IPC, set that here.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``session_map.sqlite``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_bind_port``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the port and IP for the dynamic proxy to bind to, this must
match the external configuration if dynamic_proxy_manage is set to
false.
:Default: ``8800``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_bind_ip``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the port and IP for the dynamic proxy to bind to, this must
match the external configuration if dynamic_proxy_manage is set to
false.
:Default: ``0.0.0.0``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_debug``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable verbose debugging of Galaxy-managed dynamic proxy.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_external_proxy``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The dynamic proxy is proxied by an external proxy (e.g. apache
frontend to nodejs to wrap connections in SSL).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_prefix``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Additionally, when the dynamic proxy is proxied by an upstream
server, you'll want to specify a prefixed URL so both Galaxy and
the proxy reside under the same path that your cookies are under.
This will result in a url like
https://FQDN/galaxy-prefix/gie_proxy for proxying
:Default: ``gie_proxy``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_golang_noaccess``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This attribute governs the minimum length of time between
consecutive HTTP/WS requests through the proxy, before the proxy
considers a container as being inactive and kills it.
:Default: ``60``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_golang_clean_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
In order to kill containers, the golang proxy has to check at some
interval for possibly dead containers. This is exposed as a
configurable parameter, but the default value is probably fine.
:Default: ``10``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_golang_docker_address``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The golang proxy needs to know how to talk to your docker daemon.
Currently TLS is not supported, that will come in an update.
:Default: ``unix:///var/run/docker.sock``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dynamic_proxy_golang_api_key``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The golang proxy uses a RESTful HTTP API for communication with
Galaxy instead of a JSON or SQLite file for IPC. If you do not
specify this, it will be set randomly for you. You should set this
if you are managing the proxy manually.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~
``auto_configure_logging``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If true, Galaxy will attempt to configure a simple root logger if
a "loggers" section does not appear in this configuration file.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~
``log_destination``
~~~~~~~~~~~~~~~~~~~
:Description:
Log destination, defaults to special value "stdout" that logs to
standard output. If set to anything else, then it will be
interpreted as a path that will be used as the log file, and
logging to stdout will be disabled.
:Default: ``stdout``
:Type: str
~~~~~~~~~~~~~~~~~~~
``log_rotate_size``
~~~~~~~~~~~~~~~~~~~
:Description:
Size of log file at which size it will be rotated as per the
documentation in
https://docs.python.org/library/logging.handlers.html#logging.handlers.RotatingFileHandler
If log_rotate_count is not also set, no log rotation will be
performed. A value of 0 (the default) means no rotation. Size can
be a number of bytes or a human-friendly representation like "100
MB" or "1G".
:Default: ``0``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``log_rotate_count``
~~~~~~~~~~~~~~~~~~~~
:Description:
Number of log file backups to keep, per the documentation in
https://docs.python.org/library/logging.handlers.html#logging.handlers.RotatingFileHandler
Any additional rotated log files will automatically be pruned. If
log_rotate_size is not also set, no log rotation will be
performed. A value of 0 (the default) means no rotation.
:Default: ``0``
:Type: int
~~~~~~~~~~~~~
``log_level``
~~~~~~~~~~~~~
:Description:
Verbosity of console log messages. Acceptable values can be found
here: https://docs.python.org/library/logging.html#logging-levels
A custom debug level of "TRACE" is available for even more
verbosity.
:Default: ``DEBUG``
:Type: str
~~~~~~~~~~~
``logging``
~~~~~~~~~~~
:Description:
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
:Default: ``None``
:Type: map
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_engine_option_echo``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Print database operations to the server log (warning, quite
verbose!).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``database_engine_option_echo_pool``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Print database pool operations to the server log (warning, quite
verbose!).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~
``log_events``
~~~~~~~~~~~~~~
:Description:
Turn on logging of application events and some user events to the
database.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~
``log_actions``
~~~~~~~~~~~~~~~
:Description:
Turn on logging of user actions to the database. Actions
currently logged are grid views, tool searches, and use of
"recently" used tools menu. The log_events and log_actions
functionality will eventually be merged.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~
``fluent_log``
~~~~~~~~~~~~~~
:Description:
Fluentd configuration. Various events can be logged to the
fluentd instance configured below by enabling fluent_log.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~
``fluent_host``
~~~~~~~~~~~~~~~
:Description:
Fluentd configuration. Various events can be logged to the
fluentd instance configured below by enabling fluent_log.
:Default: ``localhost``
:Type: str
~~~~~~~~~~~~~~~
``fluent_port``
~~~~~~~~~~~~~~~
:Description:
Fluentd configuration. Various events can be logged to the
fluentd instance configured below by enabling fluent_log.
:Default: ``24224``
:Type: int
~~~~~~~~~~~~~~~~~~~~~
``sanitize_all_html``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Sanitize all HTML tool output. By default, all tool output served
as 'text/html' will be sanitized thoroughly. This can be disabled
if you have special tools that require unaltered output. WARNING:
disabling this does make the Galaxy instance susceptible to XSS
attacks initiated by your users.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``sanitize_allowlist_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Datasets created by tools listed in this file are trusted and will
not have their HTML sanitized on display. This can be manually
edited or manipulated through the Admin control panel -- see
"Manage Allowlist"
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``sanitize_allowlist.txt``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``serve_xss_vulnerable_mimetypes``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
By default Galaxy will serve non-HTML tool output that may
potentially contain browser executable JavaScript content as plain
text. This will for instance cause SVG datasets to not render
properly and so may be disabled by setting this option to true.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``allowed_origin_hostnames``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Return a Access-Control-Allow-Origin response header that matches
the Origin header of the request if that Origin hostname matches
one of the strings or regular expressions listed here. This is a
comma-separated list of hostname strings or regular expressions
beginning and ending with /. E.g.
mysite.com,google.com,usegalaxy.org,/^[\w\.]*example\.com/ See:
https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``trust_jupyter_notebook_conversion``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set to true to use Jupyter nbconvert to build HTML from Jupyter
notebooks in Galaxy histories. This process may allow users to
execute arbitrary code or serve arbitrary HTML. If enabled,
Jupyter must be available and on Galaxy's PATH, to do this run
`pip install jinja2 pygments jupyter` in Galaxy's virtualenv.
:Default: ``false``
:Type: bool
~~~~~~~~~
``debug``
~~~~~~~~~
:Description:
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.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``use_access_logging_middleware``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Log request start as well as request end. Disables uvicorn access
log handler.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~
``use_lint``
~~~~~~~~~~~~
:Description:
Check for WSGI compliance.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~
``use_profile``
~~~~~~~~~~~~~~~
:Description:
Run the Python profiler on each request.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~
``use_printdebug``
~~~~~~~~~~~~~~~~~~
:Description:
Intercept print statements and show them on the returned page.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``monitor_thread_join_timeout``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When stopping Galaxy cleanly, how much time to give various
monitoring/polling threads to finish before giving up on joining
them. Set to 0 to disable this and terminate without waiting.
Among others, these threads include the job handler workers, which
are responsible for preparing/submitting and collecting/finishing
jobs, and which can cause job errors if not shut down cleanly. If
using supervisord, consider also increasing the value of
`stopwaitsecs`. See the Galaxy Admin Documentation for more.
:Default: ``30``
:Type: int
~~~~~~~~~~~~~~~~~
``use_heartbeat``
~~~~~~~~~~~~~~~~~
:Description:
Write thread status periodically to 'heartbeat.log', (careful,
uses disk space rapidly!). Useful to determine why your processes
may be consuming a lot of CPU.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~
``heartbeat_interval``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Control the period (in seconds) between dumps. Use -1 to disable.
Regardless of this setting, if use_heartbeat is enabled, you can
send a Galaxy process SIGUSR1 (`kill -USR1`) to force a dump.
:Default: ``20``
:Type: int
~~~~~~~~~~~~~~~~~
``heartbeat_log``
~~~~~~~~~~~~~~~~~
:Description:
Heartbeat log filename. Can accept the template variables
{server_name} and {pid}
:Default: ``heartbeat_{server_name}.log``
:Type: str
~~~~~~~~~~~~~~
``sentry_dsn``
~~~~~~~~~~~~~~
:Description:
Log to Sentry Sentry is an open source logging and error
aggregation platform. Setting sentry_dsn will enable the Sentry
middleware and errors will be sent to the indicated sentry
instance. This connection string is available in your sentry
instance under <project_name> -> Settings -> API Keys.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``sentry_event_level``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Determines the minimum log level that will be sent as an event to
Sentry. Possible values are DEBUG, INFO, WARNING, ERROR or
CRITICAL.
:Default: ``ERROR``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``sentry_traces_sample_rate``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set to a number between 0 and 1. With this option set, every
transaction created will have that percentage chance of being sent
to Sentry. A value higher than 0 is required to analyze
performance.
:Default: ``0.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``sentry_client_traces_sample_rate``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Sample rate for client-side (browser) performance tracing, between
0 and 1. Controls what fraction of page loads and navigations
generate performance traces sent to Sentry. Independent of
sentry_traces_sample_rate, which controls server-side tracing.
:Default: ``0.0``
:Type: float
~~~~~~~~~~~~~~~~~~~
``sentry_ca_certs``
~~~~~~~~~~~~~~~~~~~
:Description:
Use this option to provide the path to location of the CA
(Certificate Authority) certificate file if the sentry server uses
a self-signed certificate.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_statsd_middleware``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Default is true if statsd_host is set. Enable the statsd
middleware. If false and statsd_host is also set, only timing of
certain performance-critical backend tasks (e.g. the job handler
monitor loop time) data will be sent to statsd, but not web
request timing.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~
``statsd_host``
~~~~~~~~~~~~~~~
:Description:
Log to statsd Statsd is an external statistics aggregator
(https://github.com/etsy/statsd) Enabling the following options
will cause galaxy to log request timing and other statistics to
the configured statsd instance. The statsd_prefix is useful if
you are running multiple Galaxy instances and want to segment
statistics between them within the same aggregator.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~
``statsd_port``
~~~~~~~~~~~~~~~
:Description:
Log to statsd Statsd is an external statistics aggregator
(https://github.com/etsy/statsd) Enabling the following options
will cause galaxy to log request timing and other statistics to
the configured statsd instance. The statsd_prefix is useful if
you are running multiple Galaxy instances and want to segment
statistics between them within the same aggregator.
:Default: ``8125``
:Type: int
~~~~~~~~~~~~~~~~~
``statsd_prefix``
~~~~~~~~~~~~~~~~~
:Description:
Log to statsd Statsd is an external statistics aggregator
(https://github.com/etsy/statsd) Enabling the following options
will cause galaxy to log request timing and other statistics to
the configured statsd instance. The statsd_prefix is useful if
you are running multiple Galaxy instances and want to segment
statistics between them within the same aggregator.
:Default: ``galaxy``
:Type: str
~~~~~~~~~~~~~~~~~~~
``statsd_influxdb``
~~~~~~~~~~~~~~~~~~~
:Description:
If you are using telegraf to collect these metrics and then
sending them to InfluxDB, Galaxy can provide more nicely tagged
metrics. Instead of sending prefix + dot-separated-path, Galaxy
will send prefix with a tag path set to the page url
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``statsd_mock_calls``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Mock out statsd client calls - only used by testing infrastructure
really. Do not set this in production environments.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``queue_metrics_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
How often (in seconds) background observability gauges are
sampled: control-queue depth and WorkerProcess counts from the
Celery beat task, and (when enable_sse_connection_metrics is set)
active SSE-connection counts from each web worker. This is the
shared cadence for all of them. Only active when statsd_host is
set. Set to 0 to disable all background gauges.
:Default: ``15``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_sse_connection_metrics``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Emit the galaxy.sse.connections.active gauge from each web worker,
reporting how many Server-Sent Events connections that worker
currently holds (tagged by kind and server_name). Sampled on the
queue_metrics_interval cadence. Off by default so that enabling
statsd does not by itself start measuring SSE connections;
requires statsd_host to be set and queue_metrics_interval greater
than 0.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~
``library_import_dir``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Add an option to the library upload form which allows
administrators to upload a directory of files.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_library_import_dir``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Add an option to the library upload form which allows authorized
non-administrators to upload a directory of files. The configured
directory must contain sub-directories named the same as the
non-admin user's Galaxy login ( email ). The non-admin user is
restricted to uploading files or sub-directories of files
contained in their directory.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_library_import_dir_auto_creation``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If user_library_import_dir is set, this option will auto create a
library import directory for every user (based on their email)
upon login.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_library_import_symlink_allowlist``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
For security reasons, users may not import any files that actually
lie outside of their `user_library_import_dir` (e.g. using
symbolic links). A list of directories can be allowed by setting
the following option (the list is comma-separated). Be aware that
*any* user with library import permissions can import from
anywhere in these directories (assuming they are able to create
symlinks to them).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_library_import_check_permissions``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
In conjunction or alternatively, Galaxy can restrict user library
imports to those files that the user can read (by checking basic
unix permissions). For this to work, the username has to match the
username on the filesystem.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~
``allow_path_paste``
~~~~~~~~~~~~~~~~~~~~
:Description:
Allow admins to paste filesystem paths during upload. For
libraries this adds an option to the admin library upload tool
allowing admins to paste filesystem paths to files and directories
in a box, and these paths will be added to a library. For history
uploads, this allows pasting in paths as URIs. (i.e. prefixed with
file://). Set to true to enable. Please note the security
implication that this will give Galaxy Admins access to anything
your Galaxy user has access to.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``disable_library_comptypes``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Users may choose to download multiple files from a library in an
archive. By default, Galaxy allows users to select from a few
different archive formats if testing shows that Galaxy is able to
create files using these formats. Specific formats can be disabled
with this option, separate more than one format with commas.
Available formats are currently 'zip', 'gz', and 'bz2'.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~
``tool_name_boost``
~~~~~~~~~~~~~~~~~~~
:Description:
In tool search, a query match against a tool's name text will
receive this score multiplier.
:Default: ``20.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_name_exact_multiplier``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If a search query matches a tool name exactly, the score will be
multiplied by this factor.
:Default: ``10.0``
:Type: float
~~~~~~~~~~~~~~~~~
``tool_id_boost``
~~~~~~~~~~~~~~~~~
:Description:
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.
:Default: ``20.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~
``tool_section_boost``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
In tool search, a query match against a tool's section text will
receive this score multiplier.
:Default: ``3.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_description_boost``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
In tool search, a query match against a tool's description text
will receive this score multiplier.
:Default: ``8.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~
``tool_label_boost``
~~~~~~~~~~~~~~~~~~~~
:Description:
In tool search, a query match against a tool's label text will
receive this score multiplier.
:Default: ``1.0``
:Type: float
~~~~~~~~~~~~~~~~~~~
``tool_stub_boost``
~~~~~~~~~~~~~~~~~~~
:Description:
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.
:Default: ``2.0``
:Type: float
~~~~~~~~~~~~~~~~~~~
``tool_help_boost``
~~~~~~~~~~~~~~~~~~~
:Description:
In tool search, a query match against a tool's help text will
receive this score multiplier.
:Default: ``1.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~
``tool_help_bm25f_k1``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
The lower this parameter, the greater the diminishing reward for
term frequency in the help text. A higher K1 increases the level
of reward for additional occurences of a term. The default value
will provide a slight increase in score for the first, second and
third occurrence and little reward thereafter.
:Default: ``0.5``
:Type: float
~~~~~~~~~~~~~~~~~~~~~
``tool_search_limit``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Limits the number of results in toolbox search. Use to set the
maximum number of tool search results to display.
:Default: ``20``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_enable_ngram_search``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
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".
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~
``tool_ngram_minsize``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set minimum character length of ngrams
:Default: ``3``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~
``tool_ngram_maxsize``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set maximum character length of ngrams
:Default: ``4``
:Type: int
~~~~~~~~~~~~~~~~~~~~~
``tool_ngram_factor``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Ngram matched scores will be multiplied by this factor. Should
always be below 1, because an ngram match is a partial match of a
search term.
:Default: ``0.2``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_test_data_directories``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set tool test data directory. The test framework sets this value
to
'test-data,https://github.com/galaxyproject/galaxy-test-data.git'
which will cause Galaxy to clone down extra test data on the fly
for certain tools distributed with Galaxy but this is likely not
appropriate for production systems. Instead one can simply clone
that repository directly and specify a path here instead of a Git
HTTP repository.
:Default: ``test-data``
:Type: str
~~~~~~~~~~~~~
``id_secret``
~~~~~~~~~~~~~
:Description:
Galaxy encodes various internal values when these values will be
output in some format (for example, in a URL or cookie). You
should set a key to be used by the algorithm that encodes and
decodes these values. It can be any string with a length between 5
and 56 bytes. One simple way to generate a value for this is with
the shell command: python -c 'from __future__ import
print_function; import time; print(time.time())' | md5sum | cut -f
1 -d ' '
:Default: ``USING THE DEFAULT IS NOT SECURE!``
:Type: str
~~~~~~~~~~~~~~~~~~~
``use_remote_user``
~~~~~~~~~~~~~~~~~~~
:Description:
User authentication can be delegated to an upstream proxy server
(usually Apache). The upstream proxy should set a REMOTE_USER
header in the request. Enabling remote user disables regular
logins. For more information, see:
https://docs.galaxyproject.org/en/master/admin/special_topics/apache.html
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``remote_user_maildomain``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If use_remote_user is enabled and your external authentication
method just returns bare usernames, set a default mail domain to
be appended to usernames, to become your Galaxy usernames (email
addresses).
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``remote_user_header``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
If use_remote_user is enabled, the header that the upstream proxy
provides the remote username in defaults to HTTP_REMOTE_USER (the
``HTTP_`` is prepended by WSGI). This option allows you to change
the header. Note, you still need to prepend ``HTTP_`` to the
header in this option, but your proxy server should *not* include
``HTTP_`` at the beginning of the header name.
:Default: ``HTTP_REMOTE_USER``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``remote_user_secret``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
If use_remote_user is enabled, anyone who can log in to the Galaxy
host may impersonate any other user by simply sending the
appropriate header. Thus a secret shared between the upstream
proxy server, and Galaxy is required. If anyone other than the
Galaxy user is using the server, then apache/nginx should pass a
value in the header 'GX_SECRET' that is identical to the one
below.
:Default: ``USING THE DEFAULT IS NOT SECURE!``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``remote_user_logout_href``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If use_remote_user is enabled, you can set this to a URL that will
log your users out.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``post_user_logout_href``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This is the default url to which users are redirected after they
log out.
:Default: ``/root/login?is_logout_redirect=true``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``normalize_remote_user_email``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If your proxy and/or authentication source does not normalize
e-mail addresses or user names being passed to Galaxy - set this
option to true to force these to lower case.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~
``single_user``
~~~~~~~~~~~~~~~
:Description:
If an e-mail address is specified here, it will hijack remote user
mechanics (``use_remote_user``) and have the webapp inject a
single fixed user. This has the effect of turning Galaxy into a
single user application with no login or external proxy required.
Such applications should not be exposed to the world.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~
``admin_users``
~~~~~~~~~~~~~~~
:Description:
Administrative users - set this to a comma-separated list of valid
Galaxy users (email addresses). These users will have access to
the Admin section of the server, and will have access to create
users, groups, roles, libraries, and more. For more information,
see: https://galaxyproject.org/admin/
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~
``require_login``
~~~~~~~~~~~~~~~~~
:Description:
Force everyone to log in (disable anonymous access).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``show_welcome_with_login``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Show the site's welcome page (see welcome_url) alongside the login
page (even if require_login is true).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``prefer_oidc_login``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Controls the order of the login page to prefer OIDC-based login
and registration.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``allow_local_account_creation``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow unregistered users to create new local (non-OIDC) accounts
(otherwise, they will have to be created by an admin). This option
will be overridden to false in case disable_local_accounts is set
to true.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~
``disable_local_accounts``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Disable local accounts. If this option is set to true, at least
one OIDC provider needs to be configured and will serve as the
account provider. If this option is set to true,
allow_local_account creation will be overridden with false.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~
``allow_user_deletion``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow administrators to delete accounts.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``allow_user_impersonation``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow administrators to log in as other users (useful for
debugging).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``show_user_prepopulate_form``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When using LDAP for authentication, allow administrators to
pre-populate users using an additional form on 'Create new user'
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``upload_from_form_button``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If 'always-on', add another button to tool form data inputs that
allow uploading data from the tool form in fewer clicks (at the
expense of making the form more complicated). This applies to
workflows as well.
Avoiding making this a boolean because we may add options such as
'in-single-form-view' or 'in-simplified-workflow-views'.
https://github.com/galaxyproject/galaxy/pull/9809/files#r461889109
:Default: ``always-off``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``allow_user_dataset_purge``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow users to remove their datasets from disk immediately
(otherwise, datasets will be removed after a time period specified
by an administrator in the cleanup scripts run via cron)
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``new_user_dataset_access_role_default_private``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
By default, users' data will be public, but setting this to true
will cause it to be private. Does not affect existing users and
data, only ones created after this option is set. Users may still
change their default back to public.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~
``expose_user_name``
~~~~~~~~~~~~~~~~~~~~
:Description:
Expose user list. Setting this to true will expose the user list
to authenticated users. This makes sharing datasets in smaller
galaxy instances much easier as they can type a name/email and
have the correct user show up. This makes less sense on large
public Galaxy instances where that data shouldn't be exposed. For
semi-public Galaxies, it may make sense to expose just the
username and not email, or vice versa.
If enable_beta_gdpr is set to true, then this option will be
overridden and set to false.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``expose_user_email``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Expose user list. Setting this to true will expose the user list
to authenticated users. This makes sharing datasets in smaller
galaxy instances much easier as they can type a name/email and
have the correct user show up. This makes less sense on large
public Galaxy instances where that data shouldn't be exposed. For
semi-public Galaxies, it may make sense to expose just the
username and not email, or vice versa.
If enable_beta_gdpr is set to true, then this option will be
overridden and set to false.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~
``fetch_url_allowlist``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
List of allowed local network addresses for "Upload from URL"
dialog. By default, Galaxy will deny access to the local network
address space, to prevent users making requests to services which
the administrator did not intend to expose. Previously, you could
request any network service that Galaxy might have had access to,
even if the user could not normally access it. It should be a
comma-separated list of IP addresses or IP address/mask, e.g.
10.10.10.10,10.0.1.0/24,fd00::/8
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``enable_beta_gdpr``
~~~~~~~~~~~~~~~~~~~~
:Description:
Enables GDPR Compliance mode. This makes several changes to the
way Galaxy logs and exposes data externally such as removing
emails and usernames from logs and bug reports. It also causes the
delete user admin action to permanently redact their username and
password, but not to delete data associated with the account as
this is not currently easily implementable.
You are responsible for removing personal data from backups.
This forces expose_user_email and expose_user_name to be false,
and forces user_deletion to be true to support the right to
erasure.
Please read the GDPR section under the special topics area of the
admin documentation.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~
``edam_panel_views``
~~~~~~~~~~~~~~~~~~~~
:Description:
Comma-separated list of the EDAM panel views to load - choose from
merged, operations, topics. Set to empty string to disable EDAM
all together. Set default_panel_view to 'ontology:edam_topics' to
override default tool panel to use an EDAM view.
:Default: ``operations,topics``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``edam_toolbox_ontology_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Sets the path to EDAM ontology file - if the path doesn't exist
PyPI package data will be loaded.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``EDAM.tsv``
:Type: str
~~~~~~~~~~~~~~~~~~~
``panel_views_dir``
~~~~~~~~~~~~~~~~~~~
:Description:
Directory to check out for toolbox tool panel views. The path is
relative to the Galaxy root dir. To use an absolute path begin
the path with '/'. This is a comma-separated list.
:Default: ``config/plugins/activities``
:Type: str
~~~~~~~~~~~~~~~
``panel_views``
~~~~~~~~~~~~~~~
:Description:
Definitions of static toolbox panel views embedded directly in the
config instead of reading YAML from directory with
panel_views_dir.
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~
``default_panel_view``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Default tool panel view for the current Galaxy configuration. This
should refer to an id of a panel view defined using the
panel_views or panel_views_dir configuration options or an EDAM
panel view. The default panel view is simply called `default` and
refers to the tool panel state defined by the integrated tool
panel.
:Default: ``default``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``default_workflow_export_format``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Default format for the export of workflows. Possible values are
'ga' or 'format2'.
:Default: ``ga``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``parallelize_workflow_scheduling_within_histories``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If multiple job handlers are enabled, allow Galaxy to schedule
workflow invocations in multiple handlers simultaneously. This is
discouraged because it results in a less predictable order of
workflow datasets within in histories.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``maximum_workflow_invocation_duration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This is the maximum amount of time a workflow invocation may stay
in an active scheduling state in seconds. Set to -1 to disable
this maximum and allow any workflow invocation to schedule
indefinitely. The default corresponds to 1 month.
:Default: ``2678400``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``maximum_workflow_jobs_per_scheduling_iteration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Specify a maximum number of jobs that any given workflow
scheduling iteration can create. Set this to a positive integer to
prevent large collection jobs in a workflow from preventing other
jobs from executing. This may also mitigate memory issues
associated with scheduling workflows at the expense of increased
total DB traffic because model objects are expunged from the SQL
alchemy session between workflow invocation scheduling iterations.
Set to -1 to disable any such maximum.
:Default: ``1000``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~
``flush_per_n_datasets``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Maximum number of datasets to create before flushing created
datasets to database. This affects tools that create many output
datasets. Higher values will lead to fewer database flushes and
faster execution, but require more memory. Set to -1 to disable
creating datasets in batches.
:Default: ``1000``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~
``max_discovered_files``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set this to a positive integer value to limit the number of
datasets that can be discovered by a single job. This prevents
accidentally creating large numbers of datasets when running tools
that create a potentially unlimited number of output datasets,
such as tools that split a file into a collection of datasets for
each line in an input dataset.
:Default: ``10000``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``history_local_serial_workflow_scheduling``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Force serial scheduling of workflows within the context of a
particular history
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~
``enable_oidc``
~~~~~~~~~~~~~~~
:Description:
Enables and disables OpenID Connect (OIDC) support.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~
``oidc_config_file``
~~~~~~~~~~~~~~~~~~~~
:Description:
Sets the path to OIDC configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``oidc_config.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``oidc_backends_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Sets the path to OIDC backends configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``oidc_backends_config.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``oidc_auth_pipeline``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Sets the full sequence of steps that Python Social Auth goes
through when authenticating an OIDC login. Use when you want to
completely customize the pipeline (e.g. for testing).
By default, Galaxy uses galaxy.authnz.psa_authnz.AUTH_PIPELINE -
see there for example steps.
Each element should be an import path to a function, e.g.
galaxy.authnz.psa_authnz.contains_required_data
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``oidc_auth_pipeline_extra``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Sets additional authentication pipeline steps, added after the
default steps (from galaxy.authnz.psa_authnz.AUTH_PIPELINE).
Use when you want to keep the default pipeline, but add additional
custom processing.
Each element should be an import path to a function, e.g.
galaxy.authnz.psa_authnz.contains_required_data
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~
``oidc_scope_prefix``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Sets the prefix for OIDC scopes specific to this Galaxy instance.
If an API call is made against this Galaxy instance using an OIDC
bearer token, any scopes must be prefixed with this value e.g.
https://galaxyproject.org/api. More concretely, to request all
permissions that the user has, the scope would have to be
specified as "<prefix>:*". e.g "https://galaxyproject.org/api:*".
Currently, only * is recognised as a valid scope, and future
iterations may provide more fine-grained scopes.
:Default: ``https://galaxyproject.org/api``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``auth_config_file``
~~~~~~~~~~~~~~~~~~~~
:Description:
XML config file that allows the use of different authentication
providers (e.g. LDAP) instead or in addition to local
authentication (.sample is used if default does not exist).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``auth_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``api_allow_run_as``
~~~~~~~~~~~~~~~~~~~~
:Description:
Optional list of email addresses of API users who can make calls
on behalf of other users.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``bootstrap_admin_api_key``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
API key that allows performing some admin actions without actually
having a real admin user in the database and config. Only set this
if you need to bootstrap Galaxy, in particular to create a real
admin user account via API. You should probably not set this on a
production server.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``organization_name``
~~~~~~~~~~~~~~~~~~~~~
:Description:
The name of the organization that operates this Galaxy instance.
Serves as the default for the GA4GH service organization name and
can be exposed through Galaxy markdown for reports and such. For
instance, "Not Evil Corporation".
For GA4GH APIs, this is exposed via the service-info endpoint for
the Galaxy DRS API. If unset, one will be generated using
ga4gh_service_id (but only in the context of GA4GH APIs).
For more information on GA4GH service definitions - check out
https://github.com/ga4gh-discovery/ga4gh-service-registry and
https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``organization_url``
~~~~~~~~~~~~~~~~~~~~
:Description:
The URL of the organization that operates this Galaxy instance.
Serves as the default for the GA4GH service organization name and
can be exposed through Galaxy markdown for reports and such. For
instance, "notevilcorp.com".
For GA4GH APIs, this is exposed via the service-info endpoint.
For more information on GA4GH service definitions - check out
https://github.com/ga4gh-discovery/ga4gh-service-registry and
https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``ga4gh_service_id``
~~~~~~~~~~~~~~~~~~~~
:Description:
Service ID for GA4GH services (exposed via the service-info
endpoint for the Galaxy DRS API). If unset, one will be generated
using the URL the target API requests are made against.
For more information on GA4GH service definitions - check out
https://github.com/ga4gh-discovery/ga4gh-service-registry and
https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
This value should likely reflect your service's URL. For instance
for usegalaxy.org this value should be org.usegalaxy. Particular
Galaxy implementations will treat this value as a prefix and
append the service type to this ID. For instance for the DRS
service "id" (available via the DRS API) for the above
configuration value would be org.usegalaxy.drs.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``ga4gh_service_environment``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Service environment (exposed via the service-info endpoint for the
Galaxy DRS API) for implemented GA4GH services.
Suggested values are prod, test, dev, staging.
For more information on GA4GH service definitions - check out
https://github.com/ga4gh-discovery/ga4gh-service-registry and
https://editor.swagger.io/?url=https://raw.githubusercontent.com/ga4gh-discovery/ga4gh-service-registry/develop/service-registry.yaml
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``enable_tool_tags``
~~~~~~~~~~~~~~~~~~~~
:Description:
Enable tool tags (associating tools with tags). This has its own
option since its implementation has a few performance implications
on startup for large servers.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_unique_workflow_defaults``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable a feature when running workflows. When enabled, default
datasets are selected for "Set at Runtime" inputs from the history
such that the same input will not be selected twice, unless there
are more inputs than compatible datasets in the history. When
false, the most recently added compatible item in the history will
be used for each "Set at Runtime" input, independent of others in
the workflow.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``simplified_workflow_run_ui``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If set to 'off' by default, always use the traditional workflow
form that renders all steps in the GUI and serializes the tool
state of all steps during invocation. Set to 'prefer' to default
to a simplified workflow UI that only renders the inputs if
possible (the workflow must have no disconnected runtime inputs
and not replacement parameters within tool steps). In the future
'force' may be added an option for Galaskio-style servers that
should only render simplified workflows.
:Default: ``prefer``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``simplified_workflow_run_ui_target_history``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
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'.
:Default: ``prefer_current``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``simplified_workflow_run_ui_job_cache``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When the simplified workflow run form is rendered, should the
invocation use job caching. This isn't a boolean so an option for
'show-selection' can be added later.
:Default: ``off``
:Type: str
~~~~~~~~~~~~~~~~~~~
``ftp_upload_site``
~~~~~~~~~~~~~~~~~~~
:Description:
Enable Galaxy's "Upload via FTP" interface. You'll need to
install and configure an FTP server (we've used ProFTPd since it
can use Galaxy's database for authentication) and set the
following two options. This will be provided to users in the help
text as 'log in to the FTP server at '. Thus, it should be the
hostname of your FTP server.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~
``ftp_upload_dir``
~~~~~~~~~~~~~~~~~~
:Description:
This should point to a directory containing subdirectories
matching users' identifier (defaults to e-mail), where Galaxy will
look for files.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``ftp_upload_dir_identifier``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
User attribute to use as subdirectory in calculating default
ftp_upload_dir pattern. By default this will be email so a user's
FTP upload directory will be ${ftp_upload_dir}/${user.email}. Can
set this to other attributes such as id or username though.
:Default: ``email``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``ftp_upload_dir_template``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Python string template used to determine an FTP upload directory
for a particular user.
Defaults to '${ftp_upload_dir}/${ftp_upload_dir_identifier}'.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``ftp_upload_purge``
~~~~~~~~~~~~~~~~~~~~
:Description:
Set to false to prevent Galaxy from deleting uploaded FTP files as
it imports them.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~
``enable_quotas``
~~~~~~~~~~~~~~~~~
:Description:
Enable enforcement of quotas. Quotas can be set from the Admin
interface.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~
``expose_dataset_path``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This option allows users to see the full path of datasets via the
"View Details" option in the history. This option also exposes the
command line to non-administrative users. Administrators can
always see dataset paths.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_tool_source_display``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This option allows users to view the tool wrapper source code.
This is safe to enable if you have not hardcoded any secrets in
any of the tool wrappers installed on this Galaxy server. If you
have only installed tool wrappers from public tool sheds and
tools shipped with Galaxy there you can enable this option.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``job_metrics_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
YAML or XML config file that contains the job metric collection
configuration.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``job_metrics_conf.xml``
:Type: str
~~~~~~~~~~~~~~~
``job_metrics``
~~~~~~~~~~~~~~~
:Description:
Rather than specifying a job_metrics_config_file, the definition
of the metrics to enable can be embedded into Galaxy's config with
this option. This has no effect if a job_metrics_config_file is
used.
The syntax, available instrumenters, and documentation of their
options is explained in detail in the documentation:
https://docs.galaxyproject.org/en/master/admin/job_metrics.html
By default, the core plugin is enabled. Setting this option to
false or an empty list disables metrics entirely.
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``expose_potentially_sensitive_job_metrics``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This option allows users to see the job metrics (except for
environment variables).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_legacy_sample_tracking_api``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable the API for sample tracking
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_data_manager_user_view``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow non-admin users to view available Data Manager options.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``data_manager_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
File where Data Managers are configured (.sample used if default
does not exist).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``data_manager_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``shed_data_manager_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
File where Tool Shed based Data Managers are configured. This file
will be created automatically upon data manager installation.
The value of this option will be resolved with respect to
<managed_config_dir>.
:Default: ``shed_data_manager_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``galaxy_data_manager_data_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Directory to store Data Manager based tool-data. Defaults to the
value of the <tool_data_path> option.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~
``job_config_file``
~~~~~~~~~~~~~~~~~~~
:Description:
To increase performance of job execution and the web interface,
you can separate Galaxy into multiple processes. There are more
than one way to do this, and they are explained in detail in the
documentation:
https://docs.galaxyproject.org/en/master/admin/scaling.html
By default, Galaxy manages and executes jobs from within a single
process and notifies itself of new jobs via in-memory queues.
Jobs are run locally on the system on which Galaxy is started.
Advanced job running capabilities can be configured through the
job configuration file or the <job_config> option.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``job_conf.yml``
:Type: str
~~~~~~~~~~~~~~
``job_config``
~~~~~~~~~~~~~~
:Description:
Description of job running configuration, can be embedded into
Galaxy configuration or loaded from an additional file with the
job_config_file option.
:Default: ``None``
:Type: map
~~~~~~~~~~~~~~~~~~~~~~~~
``dependency_resolvers``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Rather than specifying a dependency_resolvers_config_file, the
definition of the resolvers to enable can be embedded into
Galaxy's config with this option. This has no effect if a
dependency_resolvers_config_file is used.
The syntax, available resolvers, and documentation of their
options is explained in detail in the documentation:
https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
:Default: ``None``
:Type: seq
~~~~~~~~~~~~~~~~~~~~~~~~~
``dependency_resolution``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Alternative representation of various dependency resolution
parameters. Takes the dictified version of a DependencyManager
object - so this is ideal for automating the configuration of
dependency resolution from one application that uses a
DependencyManager to another.
:Default: ``None``
:Type: map
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``default_job_resubmission_condition``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When jobs fail due to job runner problems, Galaxy can be
configured to retry these or reroute the jobs to new destinations.
Very fine control of this is available with resubmit declarations
in the job config. For simple deployments of Galaxy though, the
following attribute can define resubmission conditions for all job
destinations. If any job destination defines even one resubmission
condition explicitly in the job config - the condition described
by this option will not apply to that destination. For instance,
the condition: 'attempt < 3 and unknown_error and (time_running <
300 or time_since_queued < 300)' would retry up to two times jobs
that didn't fail due to detected memory or walltime limits but did
fail quickly (either while queueing or running). The commented out
default below results in no default job resubmission condition,
failing jobs are just failed outright.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~
``track_jobs_in_database``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This option is deprecated, use the `mem-self` handler assignment
option in the job configuration instead.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~
``use_tasked_jobs``
~~~~~~~~~~~~~~~~~~~
:Description:
This enables splitting of jobs into tasks, if specified by the
particular tool config. This is a new feature and not recommended
for production servers yet.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``local_task_queue_workers``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This enables splitting of jobs into tasks, if specified by the
particular tool config. This is a new feature and not recommended
for production servers yet.
:Default: ``2``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``job_handler_monitor_sleep``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Each Galaxy job handler process runs one thread responsible for
discovering jobs and dispatching them to runners. This thread
operates in a loop and sleeps for the given number of seconds at
the end of each iteration. This can be decreased if extremely high
job throughput is necessary, but doing so can increase CPU usage
of handler processes. Float values are allowed.
:Default: ``1.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``job_runner_monitor_sleep``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Each Galaxy job handler process runs one thread per job runner
plugin responsible for checking the state of queued and running
jobs. This thread operates in a loop and sleeps for the given
number of seconds at the end of each iteration. This can be
decreased if extremely high job throughput is necessary, but doing
so can increase CPU usage of handler processes. Float values are
allowed.
:Default: ``1.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~
``workflow_monitor_sleep``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Each Galaxy workflow handler process runs one thread responsible
for checking the state of active workflow invocations. This
thread operates in a loop and sleeps for the given number of
seconds at the end of each iteration. This can be decreased if
extremely high job throughput is necessary, but doing so can
increase CPU usage of handler processes. Float values are allowed.
:Default: ``1.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``workflow_completion_monitor_sleep``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time in seconds between workflow completion monitor iterations.
The completion monitor checks for workflows that have all jobs
completed and triggers completion hooks (e.g., exports,
notifications). Float values are allowed.
:Default: ``5.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~
``calculate_dataset_hash``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
In which cases Galaxy should calculate a hash for a new dataset.
Dataset hashes can be used by the Galaxy job cache/search to check
if job inputs match. Setting the 'enable_celery_tasks' option to
true is also required for dataset hash calculation. Possible
values are: 'always', 'upload' (the default), 'never'. If set to
'upload', the hash is calculated only for the outputs of upload
jobs.
:Default: ``upload``
:Type: str
~~~~~~~~~~~~~~~~~
``hash_function``
~~~~~~~~~~~~~~~~~
:Description:
Hash function to use if 'calculate_dataset_hash' is enabled.
Possible values are: 'md5', 'sha1', 'sha256', 'sha512'
:Default: ``sha256``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``metadata_strategy``
~~~~~~~~~~~~~~~~~~~~~
:Description:
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.
:Default: ``directory``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``retry_metadata_internally``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Although it is fairly reliable, setting metadata can occasionally
fail. In these instances, you can choose to retry setting it
internally or leave it in a failed state (since retrying
internally may cause the Galaxy process to be unresponsive). If
this option is set to false, the user will be given the option to
retry externally, or set metadata manually (when possible).
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``max_metadata_value_size``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Very large metadata values can cause Galaxy crashes. This will
allow limiting the maximum metadata key size (in bytes used in
memory, not the end result database value size) Galaxy will
attempt to save with a dataset. Use 0 to disable this feature.
The default is 5MB, but as low as 1MB seems to be a reasonable
size.
:Default: ``5242880``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``outputs_to_working_directory``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This option will override tool output paths to write outputs to
the job working directory (instead of to the file_path) and the
job manager will move the outputs to their proper place in the
dataset directory on the Galaxy server after the job completes.
This is necessary (for example) if jobs run on a cluster and
datasets can not be created by the user running the jobs (e.g. if
the filesystem is mounted read-only or the jobs are run by a
different user than the galaxy user).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``retry_job_output_collection``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If your network filesystem's caching prevents the Galaxy server
from seeing the job's stdout and stderr files when it completes,
you can retry reading these files. The job runner will retry the
number of times specified below, waiting 1 second between tries.
For NFS, you may want to try the -noac mount option (Linux) or
-actimeo=0 (Solaris).
:Default: ``0``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_evaluation_strategy``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Determines which process will evaluate the tool command line. If
set to "local" the tool command line, configuration files and
other dynamic values will be templated in the job handler process.
If set to ``remote`` the tool command line will be built as part
of the submitted job. Note that ``remote`` is a beta setting that
will be useful for materializing deferred datasets as part of the
submitted job. Note also that you have to set
``metadata_strategy`` to ``extended`` if you set this option to
``remote``.
:Default: ``local``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``preserve_python_environment``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
In the past Galaxy would preserve its Python environment when
running jobs ( and still does for internal tools packaged with
Galaxy). This behavior exposes Galaxy internals to tools and could
result in problems when activating Python environments for tools
(such as with Conda packaging). The default legacy_only will
restrict this behavior to tools identified by the Galaxy team as
requiring this environment. Set this to "always" to restore the
previous behavior (and potentially break Conda dependency
resolution for many tools). Set this to legacy_and_local to
preserve the environment for legacy tools and locally managed
tools (this might be useful for instance if you are installing
software into Galaxy's virtualenv for tool development).
:Default: ``legacy_only``
:Type: str
~~~~~~~~~~~~~~~
``cleanup_job``
~~~~~~~~~~~~~~~
:Description:
Clean up various bits of jobs left on the filesystem after
completion. These bits include the job working directory,
external metadata temporary files, and DRM stdout and stderr files
(if using a DRM). Possible values are: always, onsuccess, never
:Default: ``always``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``drmaa_external_runjob_script``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user)
this script is used to run the job script Galaxy generates for a
tool execution.
Example value 'sudo -E scripts/drmaa_external_runner.py
--assign_all_groups'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``drmaa_external_killjob_script``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user)
this script is used to kill such jobs by Galaxy (e.g. if the user
cancels the job).
Example value 'sudo -E scripts/drmaa_external_killer.py'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~
``external_chown_script``
~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user)
this script is used transfer permissions back and forth between
the Galaxy user and the user that is running the job.
Example value 'sudo -E scripts/external_chown_script.py'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``real_system_username``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
When running DRMAA jobs as the Galaxy user
(https://docs.galaxyproject.org/en/master/admin/cluster.html#submitting-jobs-as-the-real-user)
Galaxy can extract the user name from the email address (actually
the local-part before the @) or the username which are both stored
in the Galaxy data base. The latter option is particularly useful
for installations that get the authentication from LDAP. Also,
Galaxy can accept the name of a common system user (eg.
galaxy_worker) who can run every job being submitted. This user
should not be the same user running the galaxy system. Possible
values are user_email (default), username or <common_system_user>
:Default: ``user_email``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~
``environment_setup_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
File to source to set up the environment when running jobs. By
default, the environment in which the Galaxy server starts is used
when running jobs locally, and the environment set up per the
DRM's submission method and policy is used when running jobs on a
cluster (try testing with `qsub` on the command line).
environment_setup_file can be set to the path of a file on the
cluster that should be sourced by the user to set up the
environment prior to running tools. This can be especially useful
for running jobs as the actual user, to remove the need to
configure each user's environment individually.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_beta_markdown_export``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable export of Galaxy Markdown documents (pages and workflow
reports) to PDF. Requires manual installation and setup of
weasyprint (latest version available for Python 2.7 is 0.42).
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_css``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
CSS file to apply to all Markdown exports to PDF - currently used
by WeasyPrint during rendering an HTML export of the document to
PDF.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``markdown_export.css``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_css_pages``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
CSS file to apply to "Galaxy Page" exports to PDF. Generally
prefer markdown_export_css, but this is here for deployments that
would like to tailor different kinds of exports.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``markdown_export_pages.css``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_css_invocation_reports``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
CSS file to apply to invocation report exports to PDF. Generally
prefer markdown_export_css, but this is here for deployments that
would like to tailor different kinds of exports.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``markdown_export_invocation_reports.css``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_prologue``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Prologue Markdown/HTML to apply to markdown exports to PDF.
Allowing branded headers.
:Default: ``""``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_epilogue``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Prologue Markdown/HTML to apply to markdown exports to PDF.
Allowing branded footers.
:Default: ``""``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_prologue_pages``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Alternative to markdown_export_prologue that applies just to page
exports.
:Default: ``""``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_prologue_invocation_reports``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Alternative to markdown_export_prologue that applies just to
invocation report exports.
:Default: ``""``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_epilogue_pages``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Alternative to markdown_export_epilogue that applies just to page
exports.
:Default: ``""``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``markdown_export_epilogue_invocation_reports``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Alternative to markdown_export_epilogue that applies just to
invocation report exports.
:Default: ``""``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``job_resource_params_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Optional file containing job resource data entry fields
definition. These fields will be presented to users in the tool
forms and allow them to overwrite default job resources such as
number of processors, memory and walltime.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``job_resource_params_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``workflow_resource_params_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Similar to the above parameter, workflows can describe parameters
used to influence scheduling of jobs within the workflow. This
requires both a description of the fields available (which
defaults to the definitions in job_resource_params_file if not
set).
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``workflow_resource_params_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``workflow_resource_params_mapper``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
This parameter describes how to map users and workflows to a set
of workflow resource parameter to present (typically input IDs
from workflow_resource_params_file). If this this is a function
reference it will be passed various inputs (workflow model object
and user) and it should produce a list of input IDs. If it is a
path it is expected to be an XML or YAML file describing how to
map group names to parameter descriptions (additional types of
mappings via these files could be implemented but haven't yet -
for instance using workflow tags to do the mapping).
Sample default path
'config/workflow_resource_mapper_conf.yml.sample'
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``workflow_schedulers_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Optional configuration file similar to `job_config_file` to
specify which Galaxy processes should schedule workflows.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``workflow_schedulers_conf.xml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``workflow_scheduling_separate_materialization_iteration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Workflows launched with URI/URL inputs that are not marked as
'deferred' are "materialized" (or undeferred) by the workflow
scheduler. This might be a lengthy process. Setting this to 'True'
will place the invocation back in the queue after materialization
before scheduling the workflow so it is less likely to starve
other workflow scheduling. Ideally, Galaxy would allow more fine
grain control of handlers but until then, this provides a way to
tip the balance between "doing more work" and "being more fair".
The default here is pretty arbitrary - it has been to False to
optimize Galaxy for automated, single user applications where
"fairness" is mostly irrelevant.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~
``cache_user_job_count``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If using job concurrency limits (configured in job_config_file),
several extra database queries must be performed to determine the
number of jobs a user has dispatched to a given destination. By
default, these queries will happen for every job that is waiting
to run, but if cache_user_job_count is set to true, it will only
happen once per iteration of the handler queue. Although better
for performance due to reduced queries, the trade-off is a greater
possibility that jobs will be dispatched past the configured
limits if running many handlers.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``toolbox_auto_sort``
~~~~~~~~~~~~~~~~~~~~~
:Description:
If true, the toolbox will be sorted by tool id when the toolbox is
loaded. This is useful for ensuring that tools are always
displayed in the same order in the UI. If false, the order of
tools in the toolbox will be preserved as they are loaded from the
tool config files.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~
``tool_filters``
~~~~~~~~~~~~~~~~
:Description:
Define toolbox filters
(https://galaxyproject.org/user-defined-toolbox-filters/) that
admins may use to restrict the tools to display.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``tool_label_filters``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Define toolbox filters
(https://galaxyproject.org/user-defined-toolbox-filters/) that
admins may use to restrict the tool labels to display.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``tool_section_filters``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Define toolbox filters
(https://galaxyproject.org/user-defined-toolbox-filters/) that
admins may use to restrict the tool sections to display.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``user_tool_filters``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Define toolbox filters
(https://galaxyproject.org/user-defined-toolbox-filters/) that
users may use to restrict the tools to display.
:Default: ``examples:restrict_upload_to_admins, examples:restrict_encode``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_tool_section_filters``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Define toolbox filters
(https://galaxyproject.org/user-defined-toolbox-filters/) that
users may use to restrict the tool sections to display.
:Default: ``examples:restrict_text``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``user_tool_label_filters``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Define toolbox filters
(https://galaxyproject.org/user-defined-toolbox-filters/) that
users may use to restrict the tool labels to display.
:Default: ``examples:restrict_upload_to_admins, examples:restrict_encode``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``toolbox_filter_base_modules``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The base module(s) that are searched for modules for toolbox
filtering
(https://galaxyproject.org/user-defined-toolbox-filters/)
functions.
:Default: ``galaxy.tools.filters,galaxy.tools.toolbox.filters,galaxy.tool_util.toolbox.filters``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``amqp_internal_connection``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Galaxy uses AMQP internally for communicating between processes.
For example, when reloading the toolbox or locking job execution,
the process that handled that particular request will tell all
others to also reload, lock jobs, etc. For connection examples,
see
https://docs.celeryq.dev/projects/kombu/en/stable/userguide/connections.html
Without specifying anything here, galaxy will first attempt to use
your specified database_connection above. If that's not specified
either, Galaxy will automatically create and use a separate sqlite
database located in your <galaxy>/database folder (indicated in
the commented out line below).
:Default: ``sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~
``enable_celery_tasks``
~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Offload long-running tasks to a Celery task queue. Activate this
only if you have setup a Celery worker for Galaxy and you have
configured the `celery_conf` option below. Specifically, you need
to set the `result_backend` option in the `celery_conf` option to
a valid Celery result backend URL. By default, Galaxy uses an
SQLite database at '<data_dir>/results.sqlite' for storing task
results. For details, see
https://docs.galaxyproject.org/en/master/admin/production.html#use-celery-for-asynchronous-tasks
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~
``enable_tool_requests``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Submit tool jobs through the asynchronous tool requests API
(`/api/jobs`) when available. The client falls back to the legacy
`/api/tools` endpoint when this is disabled, when Celery is not
enabled, or when the tool does not provide a typed parameter
schema.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~
``celery_conf``
~~~~~~~~~~~~~~~
:Description:
Configuration options passed to Celery.
To refer to a task by name, use the template `galaxy.foo` where
`foo` is the function name of the task defined in the
galaxy.celery.tasks module.
The `broker_url` option, if unset or null, defaults to the value
of `amqp_internal_connection`. The `result_backend` option, if
unset or null, defaults to an SQLite database at
'<data_dir>/results.sqlite' for storing task results. Please use a
more robust backend (e.g. Redis) for production setups.
The galaxy.fetch_data task can be disabled by setting its route to
"disabled": `galaxy.fetch_data: disabled`. (Other tasks cannot be
disabled on a per-task basis at this time.)
For details, see Celery documentation at
https://docs.celeryq.dev/en/stable/userguide/configuration.html.
:Default: ``{'broker_url': None, 'result_backend': None, 'task_routes': {'galaxy.fetch_data': 'galaxy.external', 'galaxy.set_job_metadata': 'galaxy.external'}}``
:Type: any
~~~~~~~~~~~~~~~~~~~~~~~~~~
``celery_user_rate_limit``
~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
If set to a non-0 value, upper limit on number of tasks that can
be executed per user per second.
:Default: ``0.0``
:Type: float
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``celery_user_concurrency_limit``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Maximum number of Celery tasks that can execute concurrently for a
single user. If set to 0 (default), no concurrency limit is
enforced. When a user exceeds this limit, new tasks are deferred
and retried until a slot becomes available. A periodic cleanup
task reclaims slots from crashed workers by inspecting active
tasks on all workers.
:Default: ``0``
:Type: int
~~~~~~~~~~~~~~
``use_pbkdf2``
~~~~~~~~~~~~~~
:Description:
Allow disabling pbkdf2 hashing of passwords for legacy situations.
This should normally be left enabled unless there is a specific
reason to disable it.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~
``cookie_domain``
~~~~~~~~~~~~~~~~~
:Description:
Tell Galaxy that multiple domains sharing the same root are
associated to this instance and wants to share the same session
cookie. This allow a user to stay logged in when passing from one
subdomain to the other. This root domain will be written in the
unique session cookie shared by all subdomains.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``select_type_workflow_threshold``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Due to performance considerations (select2 fields are pretty
'expensive' in terms of memory usage) Galaxy uses the regular
select fields for non-dataset selectors in the workflow run form.
use 0 in order to always use select2 fields, use -1 (default) in
order to always use the regular select fields, use any other
positive number as threshold (above threshold: regular select
fields will be used)
:Default: ``-1``
:Type: int
~~~~~~~~~~~~~~
``ai_api_key``
~~~~~~~~~~~~~~
:Description:
API key for an AI provider. AI provider is Openai By default
(https://openai.com/) to enable the wizard (or more?)
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~
``ai_api_base_url``
~~~~~~~~~~~~~~~~~~~
:Description:
AI API base URL. Needs to be OpenAI compatible, defaults to OpenAI
:Default: ``None``
:Type: str
~~~~~~~~~~~~
``ai_model``
~~~~~~~~~~~~
:Description:
AI model to enable the wizard. Global fallback for all AI agents.
:Default: ``gpt-4o``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``inference_services``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configuration for AI inference services used by agents and
visualization plugins. Supports per-agent or per-plugin model,
temperature, max_tokens, retries, api_key, api_base_url, and
enabled settings. Valid keys include agent types (e.g. router,
error_analysis) and plugin names (e.g. jupyterlite). Agents and
plugins inherit from 'default' configuration, which itself falls
back to global ai_model/ai_api_key settings. All agents are
enabled by default. Example: inference_services: { default: {
model: gpt-4o-mini, temperature: 0.7 }, custom_tool: { enabled:
false }, jupyterlite: { model: gpt-4o } } Set static_responses to
a YAML file path to replace all LLM calls with deterministic
responses for testing: inference_services: { static_responses:
test/integration/static_agents.yml } Per-agent or default-block
``structured_output_override: true|false`` beats the model
capability table -- see ``agent_model_capabilities_file`` for the
table's location and contents. Per-agent or default-block
``retries`` sets the pydantic-ai retry budget (tool calls and
output validation); it defaults to 3. Raise it if a model
intermittently fails to produce conforming output ("Exceeded
maximum output retries"). custom_tool's producer keeps a budget of
0 because it runs its own reflection loop; a shared ``default``
block does not change that -- set ``custom_tool.retries``
explicitly to override it.
:Default: ``None``
:Type: any
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``agent_model_capabilities_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
YAML file with capability hints for agent inference models. Maps
fnmatch-style globs against model names to features such as
structured-output (tool-calling / JSON-mode) support. Galaxy ships
a sample populated with common model families; admins can drop a
file named ``agent_model_capabilities.yml`` in ``config_dir`` to
override the shipped table for private models.
``inference_services`` ``structured_output_override`` overrides
this table for a specific agent or default block.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``agent_model_capabilities.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``gtn_database_path``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to the SQLite FTS5 database used by the GTN training agent.
Resolves against ``data_dir`` so admins can place it in a
mutable-data directory. The file is downloaded automatically on
first use from ``gtn_database_url`` if it does not exist.
The value of this option will be resolved with respect to
<data_dir>.
:Default: ``gtn/gtn_search.db``
:Type: str
~~~~~~~~~~~~~~~~~~~~
``gtn_database_url``
~~~~~~~~~~~~~~~~~~~~
:Description:
URL used to download the GTN search database when the local file
at ``gtn_database_path`` is missing.
:Default: ``https://depot.galaxyproject.org/chatgxy/gtn_search.db``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``gtn_database_refresh_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time (in seconds) between celery-beat triggered freshness checks
of the GTN search database from ``gtn_database_url``. The task
HEADs depot and only re-downloads when its ``Last-Modified`` is
newer than the local file -- steady-state cost is a few hundred
bytes per tick. When a download does happen it atomically replaces
``gtn_database_path``; live handlers pick up the new copy on their
next query since GTNSearchDB opens a read-only connection per
call. Only registered when ``inference_services`` is configured
(i.e. GalaxyAI is in use). Set to 0 to disable automatic refresh
-- admins can still refresh on demand via ``python -m
galaxy.agents.gtn --refresh``. Requires celery.
:Default: ``86400``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``iwc_manifest_refresh_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time (in seconds) between celery-beat triggered refreshes of the
in-process IWC workflow manifest cache used by the agent-ops
layer. Default matches the cache's in-process TTL so the cache
stays continuously warm rather than expiring between user-driven
hits. Failures are logged and the prior cached copy is retained.
Only registered when ``inference_services`` is configured (i.e.
GalaxyAI is in use). Set to 0 to disable automatic refresh --
agent-ops callers will then fall back to lazy on-demand fetching
with the same hour TTL. Requires celery.
:Default: ``3600``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_tool_recommendations``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Allow the display of tool recommendations in workflow editor and
after tool execution. If it is enabled and set to true, please
enable 'tool_recommendation_model_path' as well
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_recommendation_model_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set remote path of the trained model (HDF5 file) for tool
recommendation.
:Default: ``https://github.com/galaxyproject/galaxy-test-data/raw/master/tool_recommendation_model_v_0.2.hdf5``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~
``topk_recommendations``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the number of predictions/recommendations to be made by the
model
:Default: ``20``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``admin_tool_recommendations_path``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set path to the additional tool preferences from Galaxy admins. It
has two blocks. One for listing deprecated tools which will be
removed from the recommendations and another is for adding
additional tools to be recommended along side those from the deep
learning model.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_recommendations_overwrite.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``overwrite_model_recommendations``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Overwrite or append to the tool recommendations by the deep
learning model. When set to true, all the recommendations by the
deep learning model are overwritten by the recommendations set by
an admin in a config file 'tool_recommendations_overwrite.yml'.
When set to false, the recommended tools by admins and predicted
by the deep learning model are shown.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``error_report_file``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to error reports configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``error_report.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_destinations_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Path to dynamic tool destinations configuration file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``tool_destinations.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``welcome_directory``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Location of New User Welcome data, a single directory containing
the images and JSON of Topics/Subtopics/Slides as export. This
location is relative to galaxy/static
:Default: ``plugins/welcome_page/new_user/static/topics/``
:Type: str
~~~~~~~~~~~~~~~~~~~~~
``vault_config_file``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Vault config file.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``vault_conf.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``vault_token_renewal_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Time (in seconds) between Hashicorp Vault token renewal attempts.
Set to 0 to disable automatic token renewal (the default). When
enabled, a Celery Beat periodic task will call Vault's renew-self
endpoint at this interval. Recommended value: half the token TTL
(e.g. 1800 for a 1-hour TTL token). Requires Celery Beat to be
running.
:Default: ``0``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~
``url_headers_config_file``
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Configuration file for URL request headers allow-list with URL
pattern matching. This file defines which HTTP headers are allowed
in URL fetch requests based on URL patterns, and whether they
should be treated as sensitive (encrypted in the vault) or not. If
no allow-list is specified, no headers will be allowed in URL
requests. This provides fine-grained security control over what
headers can be sent when Galaxy fetches external URLs on behalf of
users, allowing different headers for different target domains or
services.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``url_headers_conf.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``display_builtin_converters``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Display built-in converters in the tool panel.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~
``themes_config_file``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Optional file containing one or more themes for galaxy. If several
themes are defined, users can choose their preferred theme in the
client.
The value of this option will be resolved with respect to
<config_dir>.
:Default: ``themes_conf.yml``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_beacon_integration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enables user preferences and api endpoint for the beacon
integration.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_training_recommendations``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Displays a link to training material, if any includes the current
tool. When activated the following options also need to be set:
tool_training_recommendations_link,
tool_training_recommendations_api_url
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_training_recommendations_link``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Template URL to display all tutorials containing current tool.
Valid template inputs are: {repository_owner} {name}
{tool_id} {training_tool_identifier} {version}
:Default: ``https://training.galaxyproject.org/training-material/by-tool/{training_tool_identifier}.html``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``tool_training_recommendations_api_url``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
URL to API describing tutorials containing specific tools. When
CORS is used, make sure to add this host.
:Default: ``https://training.galaxyproject.org/training-material/api/top-tools.json``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``citations_export_message_html``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Message to display on the export citations tool page
:Default: ``When writing up your analysis, remember to include all references that should be cited in order to completely describe your work. Also, please remember to <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~
``enable_sse_updates``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enables real-time updates via Server-Sent Events (SSE), replacing
the history (3 s), entry-point (10 s) and notification (30 s)
polling loops with push events delivered over a single
``/api/events/stream`` connection per browser tab. A background
monitor watches for history changes (via PostgreSQL LISTEN/NOTIFY,
or audit-table polling as a fallback for SQLite); entry-point
changes are dispatched directly from the code paths that mutate
them; in-app notifications and broadcasts are pushed when
``enable_notification_system`` is also true. When disabled,
polling remains the source of updates for all three. See the admin
guide "Server-Sent Events for real-time updates" for the full
architecture, monitoring guidance and proxy configuration.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``history_audit_monitor_poll_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The interval in seconds between history audit table polls when
using the polling fallback (SQLite or when PostgreSQL
LISTEN/NOTIFY is unavailable). Only used when enable_sse_updates
is true. Lower values mean faster updates but more database
queries. Recommended range: 1-5 seconds.
:Default: ``2``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_notification_system``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enables the Notification System integrated in Galaxy.
Users can receive automatic notifications when a certain resource
is shared with them or when some long running operations have
finished, etc.
The system allows notification scheduling and expiration, and
users can opt-out of specific notification categories or channels.
Delivery is push-based via Server-Sent Events when
``enable_sse_updates`` is also true, and falls back to 30-second
polling against ``/api/notifications/status`` otherwise.
Admins can schedule and broadcast notifications that will be
visible to all users, including special server-wide announcements
such as scheduled maintenance, high load warnings, and event
announcements, to name a few examples.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~
``enable_mcp_server``
~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable the Model Context Protocol (MCP) server integration.
MCP allows AI assistants (like Claude, ChatGPT, etc.) to interact
with Galaxy programmatically through a standardized protocol. When
enabled, Galaxy exposes an MCP endpoint that provides tools for
searching, executing tools, managing histories, and more.
The MCP server requires API key authentication and uses the
existing Galaxy REST API internally. This feature is experimental
and disabled by default.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~
``mcp_server_path``
~~~~~~~~~~~~~~~~~~~
:Description:
URL path where the MCP server endpoint will be mounted (default:
/api/mcp).
This setting only takes effect when 'enable_mcp_server' is true.
The MCP endpoint will be accessible at this path relative to the
Galaxy base URL.
:Default: ``/api/mcp``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``expired_notifications_cleanup_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The interval in seconds between attempts to delete all expired
notifications from the database (every 24 hours by default). Runs
in a Celery task.
:Default: ``86400``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``dispatch_notifications_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The interval in seconds between attempts to dispatch notifications
to users (every 10 minutes by default). Runs in a Celery task.
:Default: ``600``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~
``help_forum_api_url``
~~~~~~~~~~~~~~~~~~~~~~
:Description:
The URL pointing to the Galaxy Help Forum API base URL. The API
must be compatible with Discourse API
(https://docs.discourse.org/).
:Default: ``https://help.galaxyproject.org/``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_help_forum_tool_panel_integration``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable the integration of the Galaxy Help Forum in the tool panel.
This requires the help_forum_api_url to be set.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_temp_dir``
~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Directory to store temporary files for file sources. This defaults
to new_file_path if not set.
:Default: ``None``
:Type: str
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_webdav_use_temp_files``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Deprecated. This option is ignored by the fsspec-based WebDAV file
source.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``file_source_listings_expiry_time``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Number of seconds before file source content listings are
refreshed. Shorter times will result in more queries while
browsing a file sources. Longer times will result in fewer
requests to file sources but outdated contents might be displayed
to the user. Currently only affects s3fs file sources.
:Default: ``60``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``install_tool_dependencies``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the default value in the Admin UI to automatically install
tool dependencies when installing tools from the Tool Shed or not.
Tool dependencies are the software packages and libraries required
for a tool to function properly. Tool dependencies are typically
specified in the tool's XML configuration using <requirement>
tags. Galaxy can automatically install these dependencies if the
tool_dependency_dir is properly configured in the galaxy.yml file.
This option should be set to false if containerized versions of
tools are used.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``install_repository_dependencies``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the default value in the Admin UI to automatically install
repository dependencies when installing tools from the Tool Shed.
Repository dependencies are other Tool Shed repositories that the
tool being installed depends on and they are commonly used with
tool suites. Repository dependencies ensure that all necessary
components are installed for the tool (or suite) to work correctly
within the Galaxy environment.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``install_resolver_dependencies``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Set the default value in the Admin UI to automatically install
resolver dependencies when installing tools from the Tool Shed.
Resolver dependencies is a mechanism used by Galaxy to locate and
make available the required software packages for Galaxy tools.
Galaxy uses dependency resolvers (e.g., Conda) to determine how to
satisfy these dependencies. This option should be set to false if
containerized versions of tools are used.
:Default: ``true``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_failed_jobs_working_directory_cleanup``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enables the cleanup of failed Galaxy job's working directories.
Runs in a Celery task.
:Default: ``false``
:Type: bool
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``failed_jobs_working_directory_cleanup_days``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The number of days to keep failed Galaxy job's working directories
before attempting to delete them if
enable_failed_jobs_working_directory_cleanup is ``true``. Runs in
a Celery task.
:Default: ``5``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``failed_jobs_working_directory_cleanup_interval``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
The interval in seconds between attempts to delete all failed
Galaxy job's working directories from the filesystem (every 24
hours by default) if enable_failed_jobs_working_directory_cleanup
is ``true``. Runs in a Celery task.
:Default: ``86400``
:Type: int
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
``enable_beta_tool_formats``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:Description:
Enable beta tool formats (yaml, cwl, ...) which is a prerequisite
for user defined tools.
:Default: ``false``
:Type: bool
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