Galaxy Deployment & Administration

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
- Template Variable Validators
- Connecting Configuration Templates to Secrets
- OAuth 2.0 Enabled Configurations
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
- 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?
User-Defined Tools (Beta)
- Differences from Standard Galaxy Tools
- Enabling User-Defined Tools
- Sharing User-Defined Tools
- Security considerations
- Limitations
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
- Deleting old galaxy_session records
- Deleting old job metrics
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_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
- enable_tool_generated_tours
- 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
- 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
- email_ban_file
- canonical_email_rules
- 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
- interactivetoolsproxy_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
- citation_bibtex
- release_doc_base_url
- screencasts_url
- terms_url
- static_enabled
- static_cache_time
- static_dir
- static_dist_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_local_account_creation
- disable_local_accounts
- 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_auth_pipeline
- oidc_auth_pipeline_extra
- 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
- calculate_dataset_hash
- hash_function
- 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
- workflow_scheduling_separate_materialization_iteration
- 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
- ai_api_key
- ai_api_base_url
- ai_model
- 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
- file_source_temp_dir
- file_source_webdav_use_temp_files
- file_source_listings_expiry_time
- install_tool_dependencies
- install_repository_dependencies
- install_resolver_dependencies
- enable_failed_jobs_working_directory_cleanup
- failed_jobs_working_directory_cleanup_days
- failed_jobs_working_directory_cleanup_interval
Migrating from uWSGI to Gunicorn and FastAPI
- Why we migrated away from uWSGI
- How do I upgrade my instance to use Gunicorn