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
  • 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