Galaxy Deployment & Administration

This documentation is in the midst of being ported and unified based on resources from old wiki and new hub. These resources should be used together for now.

Supported Python versions
Framework Dependencies
- How it works
- Options
- Managing dependencies manually
- Dependency management complications
- Adding additional Galaxy dependencies
Galaxy Configuration
- Overview
- Configuration Files
- Configuration Basics
- Configuration Options
Logging Configuration
- Overview
- Basic Configuration
- Advanced Configuration
Production Environments
- Why bother?
- Groundwork for scalability
- Basic configuration
- Advanced configuration
Connecting Users and Data
- Datasets vs Files
- Object Store Templates
- File Source Templates
- Playing Nicer with Ansible
- Jinja Template Reference
- Connecting Configuration Templates to Secrets
Security considerations
- Protect Galaxy against data loss due to misbehaving tools
Proxying Galaxy with NGINX
- Prerequisites
- Basic Configuration
- Advanced Configuration Topics
Proxying Galaxy with Apache
- Prerequisites
- Basic configuration
- Advanced Configuration Topics
Scaling and Load Balancing
- Terminology
- Application Servers
- Deployment Options
- Job Handler Assignment Methods
- Configuration
- gravity & galaxyctl
- Logging and daemonization
- Starting and Stopping
Connecting to a Cluster
- Distributed Resources Managers
- Preliminary Setup
- Runner Configuration
- Submitting Jobs as the Real User
- Special environment variables for job resources
- Contributors
Galaxy Job Configuration
- job_conf.xml Syntax
- Mapping Tools To Destinations
- Limiting Job Resource Usage
Collecting Job Metrics
- Default Job Metrics Configuration
- Available Job Metrics Plugins
- Overriding the Global Job Metrics Configuration
Authentication
- Galaxy Database
- OIDC and OAuth2.0
- Authentication Framework
- Remote User Authentication
- User Activation
- Authentication Related Code
Tool Panel Administration
- Configuration
- Layout
- Tool panel views
Tool data
- History
- Tool data
- loc files
- Tool data tables
Message queue
- Transports
Dependency Resolvers in Galaxy
- Default Dependency Resolvers
Containers in Galaxy
- Container Resolvers in Galaxy
- Configuration:
- Main resolver types:
- Function and use of the resolve function of the main resolver types:
- Additional resolver types
- Building resolver types:
- Parameters:
- Note on the built-in caching capabilities of singularity and docker
- Other considerations
Conda for Tool Dependencies
- 1. How do I enable Conda dependency resolution for Galaxy tools?
- 2. How do Conda dependencies work? Where do things get installed?
- 3. What is required to make use of this? Any specific packages, Galaxy revision, OS version, etc.?
- 4. If I have Conda enabled, what do I need to do to install tools using it? For example, how can I install the latest Trinity? And how will I know the dependencies are installed?
- 5. Can I mix traditional Galaxy packages and Conda packages?
- 6. How do I know what system is being used by a given tool?
- 7. How do I go about specifying Conda dependencies for a tool? All the docs still seem to recommend (or exclusively discuss) the tool_dependencies.xml method.
- 8. During tool installation what if there is no Conda package available for a given requirement? What if the requirement is resolved in a different software than the original wrapper author meant to use?
- 9. Where can I find a list of existing Conda packages that I can point to, so I don’t have to reinvent the wheel for common dependencies?
- 10. How can I create a new Conda package for a dependency?
- 11. Is there a way to convert traditional Tool Shed package recipes that are not yet in a Conda channel?
- 12. What is the recommendation for existing installations? Will I continue to maintain both systems or migrate to the new Conda system eventually?
- 13. What can I do about this placehold error?
- 14. What can I do about this LOCKERROR error?
- 15. What can I do about linking errors?
- 16. What can I do if Conda doesn’t work for me?
- 17. How can I upgrade Conda?
Galaxy Database Schema Migrations
- Administering Galaxy: upgrading and downgrading the database
- Advanced usage
- Developing Galaxy: creating new revisions
- Troubleshooting
Galaxy Reports
- Overview
- Configuration
Scripts & Tricks
- Uploading a directory into a Data Library
- Deleting unused histories
Configuration Options
- config_dir
- managed_config_dir
- data_dir
- templates_dir
- cache_dir
- database_connection
- database_engine_option_pool_size
- database_engine_option_max_overflow
- database_engine_option_pool_recycle
- database_engine_option_server_side_cursors
- database_query_profiling_proxy
- database_template
- database_log_query_counts
- slow_query_log_threshold
- enable_per_request_sql_debugging
- install_database_connection
- database_auto_migrate
- database_wait
- database_wait_attempts
- database_wait_sleep
- history_audit_table_prune_interval
- file_path
- new_file_path
- maximum_upload_file_size
- tool_config_file
- shed_tool_config_file
- migrated_tools_config
- integrated_tool_panel_config
- tool_path
- tool_dependency_dir
- dependency_resolvers_config_file
- conda_prefix
- conda_exec
- conda_debug
- conda_ensure_channels
- conda_use_local
- conda_auto_install
- conda_auto_init
- conda_copy_dependencies
- local_conda_mapping_file
- modules_mapping_files
- use_cached_dependency_manager
- tool_dependency_cache_dir
- precache_dependencies
- tool_sheds_config_file
- watch_tools
- watch_job_rules
- watch_core_config
- watch_tours
- short_term_storage_dir
- short_term_storage_default_duration
- short_term_storage_maximum_duration
- short_term_storage_cleanup_interval
- file_sources_config_file
- file_sources
- object_store_templates_config_file
- object_store_templates
- file_source_templates_config_file
- file_source_templates
- user_config_templates_index_by
- user_config_templates_use_saved_configuration
- enable_mulled_containers
- container_resolvers_config_file
- container_resolvers
- involucro_path
- involucro_auto_init
- mulled_channels
- enable_tool_shed_check
- hours_between_check
- tool_data_table_config_path
- shed_tool_data_table_config
- tool_data_path
- shed_tool_data_path
- watch_tool_data_dir
- refgenie_config_file
- build_sites_config_file
- builds_file_path
- len_file_path
- datatypes_config_file
- sniff_compressed_dynamic_datatypes_default
- datatypes_disable_auto
- visualization_plugins_directory
- tour_config_dir
- webhooks_dir
- job_working_directory
- template_cache_path
- check_job_script_integrity
- check_job_script_integrity_count
- check_job_script_integrity_sleep
- default_job_shell
- enable_tool_document_cache
- tool_search_index_dir
- biotools_content_directory
- biotools_use_api
- biotools_service_cache_type
- biotools_service_cache_data_dir
- biotools_service_cache_lock_dir
- biotools_service_cache_url
- biotools_service_cache_table_name
- biotools_service_cache_schema_name
- citation_cache_type
- citation_cache_data_dir
- citation_cache_lock_dir
- citation_cache_url
- citation_cache_table_name
- citation_cache_schema_name
- mulled_resolution_cache_type
- mulled_resolution_cache_data_dir
- mulled_resolution_cache_lock_dir
- mulled_resolution_cache_expire
- mulled_resolution_cache_url
- mulled_resolution_cache_table_name
- mulled_resolution_cache_schema_name
- object_store_config_file
- object_store_config
- object_store_cache_monitor_driver
- object_store_cache_monitor_interval
- object_store_cache_path
- object_store_cache_size
- object_store_always_respect_user_selection
- object_store_store_by
- smtp_server
- smtp_username
- smtp_password
- smtp_ssl
- mailing_join_addr
- mailing_join_subject
- mailing_join_body
- error_email_to
- email_from
- custom_activation_email_message
- instance_resource_url
- instance_access_url
- email_domain_blocklist_file
- email_domain_allowlist_file
- registration_warning_message
- user_activation_on
- activation_grace_period
- inactivity_box_content
- password_expiration_period
- enable_account_interface
- session_duration
- ga_code
- plausible_server
- plausible_domain
- matomo_server
- matomo_site_id
- display_servers
- enable_old_display_applications
- aws_estimate
- carbon_emission_estimates
- geographical_server_location_code
- power_usage_effectiveness
- interactivetools_enable
- interactivetools_upstream_proxy
- interactivetools_proxy_host
- interactivetools_base_path
- interactivetools_map
- interactivetools_prefix
- retry_interactivetool_metadata_internally
- visualizations_visible
- message_box_visible
- message_box_content
- message_box_class
- brand
- display_galaxy_brand
- pretty_datetime_format
- trs_servers_config_file
- user_preferences_extra_conf_path
- default_locale
- galaxy_url_prefix
- galaxy_infrastructure_url
- galaxy_infrastructure_web_port
- welcome_url
- logo_url
- logo_src
- logo_src_secondary
- helpsite_url
- wiki_url
- quota_url
- support_url
- citation_url
- release_doc_base_url
- screencasts_url
- terms_url
- static_enabled
- static_cache_time
- static_dir
- static_images_dir
- static_favicon_dir
- static_scripts_dir
- static_style_dir
- static_robots_txt
- display_chunk_size
- apache_xsendfile
- nginx_x_accel_redirect_base
- upstream_gzip
- upstream_mod_zip
- x_frame_options
- nginx_upload_store
- nginx_upload_path
- nginx_upload_job_files_store
- nginx_upload_job_files_path
- tus_upload_store
- tus_upload_store_job_files
- chunk_upload_size
- dynamic_proxy_manage
- dynamic_proxy
- dynamic_proxy_session_map
- dynamic_proxy_bind_port
- dynamic_proxy_bind_ip
- dynamic_proxy_debug
- dynamic_proxy_external_proxy
- dynamic_proxy_prefix
- dynamic_proxy_golang_noaccess
- dynamic_proxy_golang_clean_interval
- dynamic_proxy_golang_docker_address
- dynamic_proxy_golang_api_key
- auto_configure_logging
- log_destination
- log_rotate_size
- log_rotate_count
- log_level
- logging
- database_engine_option_echo
- database_engine_option_echo_pool
- log_events
- log_actions
- fluent_log
- fluent_host
- fluent_port
- sanitize_all_html
- sanitize_allowlist_file
- serve_xss_vulnerable_mimetypes
- allowed_origin_hostnames
- trust_jupyter_notebook_conversion
- debug
- use_access_logging_middleware
- use_lint
- use_profile
- use_printdebug
- monitor_thread_join_timeout
- use_heartbeat
- heartbeat_interval
- heartbeat_log
- sentry_dsn
- sentry_event_level
- sentry_traces_sample_rate
- sentry_ca_certs
- statsd_host
- statsd_port
- statsd_prefix
- statsd_influxdb
- statsd_mock_calls
- library_import_dir
- user_library_import_dir
- user_library_import_dir_auto_creation
- user_library_import_symlink_allowlist
- user_library_import_check_permissions
- allow_path_paste
- disable_library_comptypes
- tool_name_boost
- tool_name_exact_multiplier
- tool_id_boost
- tool_section_boost
- tool_description_boost
- tool_label_boost
- tool_stub_boost
- tool_help_boost
- tool_help_bm25f_k1
- tool_search_limit
- tool_enable_ngram_search
- tool_ngram_minsize
- tool_ngram_maxsize
- tool_ngram_factor
- tool_test_data_directories
- id_secret
- use_remote_user
- remote_user_maildomain
- remote_user_header
- remote_user_secret
- remote_user_logout_href
- post_user_logout_href
- normalize_remote_user_email
- single_user
- admin_users
- require_login
- show_welcome_with_login
- prefer_custos_login
- allow_user_creation
- allow_user_deletion
- allow_user_impersonation
- show_user_prepopulate_form
- upload_from_form_button
- allow_user_dataset_purge
- new_user_dataset_access_role_default_private
- expose_user_name
- expose_user_email
- fetch_url_allowlist
- enable_beta_gdpr
- enable_beta_workflow_modules
- edam_panel_views
- edam_toolbox_ontology_path
- panel_views_dir
- panel_views
- default_panel_view
- default_workflow_export_format
- parallelize_workflow_scheduling_within_histories
- maximum_workflow_invocation_duration
- maximum_workflow_jobs_per_scheduling_iteration
- flush_per_n_datasets
- max_discovered_files
- history_local_serial_workflow_scheduling
- enable_oidc
- oidc_config_file
- oidc_backends_config_file
- oidc_scope_prefix
- auth_config_file
- api_allow_run_as
- bootstrap_admin_api_key
- organization_name
- organization_url
- ga4gh_service_id
- ga4gh_service_environment
- enable_tool_tags
- enable_unique_workflow_defaults
- simplified_workflow_run_ui
- simplified_workflow_run_ui_target_history
- simplified_workflow_run_ui_job_cache
- ftp_upload_site
- ftp_upload_dir
- ftp_upload_dir_identifier
- ftp_upload_dir_template
- ftp_upload_purge
- enable_quotas
- expose_dataset_path
- enable_tool_source_display
- job_metrics_config_file
- job_metrics
- expose_potentially_sensitive_job_metrics
- enable_legacy_sample_tracking_api
- enable_data_manager_user_view
- data_manager_config_file
- shed_data_manager_config_file
- galaxy_data_manager_data_path
- job_config_file
- job_config
- dependency_resolvers
- dependency_resolution
- default_job_resubmission_condition
- track_jobs_in_database
- use_tasked_jobs
- local_task_queue_workers
- job_handler_monitor_sleep
- job_runner_monitor_sleep
- workflow_monitor_sleep
- metadata_strategy
- retry_metadata_internally
- max_metadata_value_size
- outputs_to_working_directory
- retry_job_output_collection
- tool_evaluation_strategy
- preserve_python_environment
- cleanup_job
- drmaa_external_runjob_script
- drmaa_external_killjob_script
- external_chown_script
- real_system_username
- environment_setup_file
- enable_beta_markdown_export
- markdown_export_css
- markdown_export_css_pages
- markdown_export_css_invocation_reports
- markdown_export_prologue
- markdown_export_epilogue
- markdown_export_prologue_pages
- markdown_export_prologue_invocation_reports
- markdown_export_epilogue_pages
- markdown_export_epilogue_invocation_reports
- job_resource_params_file
- workflow_resource_params_file
- workflow_resource_params_mapper
- workflow_schedulers_config_file
- cache_user_job_count
- toolbox_auto_sort
- tool_filters
- tool_label_filters
- tool_section_filters
- user_tool_filters
- user_tool_section_filters
- user_tool_label_filters
- toolbox_filter_base_modules
- amqp_internal_connection
- enable_celery_tasks
- celery_conf
- celery_user_rate_limit
- use_pbkdf2
- cookie_domain
- select_type_workflow_threshold
- enable_tool_recommendations
- tool_recommendation_model_path
- topk_recommendations
- admin_tool_recommendations_path
- overwrite_model_recommendations
- error_report_file
- tool_destinations_config_file
- welcome_directory
- vault_config_file
- display_builtin_converters
- themes_config_file
- enable_beacon_integration
- tool_training_recommendations
- tool_training_recommendations_link
- tool_training_recommendations_api_url
- citations_export_message_html
- enable_notification_system
- expired_notifications_cleanup_interval
- dispatch_notifications_interval
- help_forum_api_url
- enable_help_forum_tool_panel_integration
Migrating from uWSGI to Gunicorn and FastAPI
- Why we migrated away from uWSGI
- How do I upgrade my instance to use Gunicorn