Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
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
- Galaxy Configuration
- Logging Configuration
- Production Environments
- Proxying Galaxy with NGINX
- Proxying Galaxy with Apache
- Scaling and Load Balancing
- Connecting to a Cluster
- Galaxy Job Configuration
- Authentication
- Tool Panel Administration
- Message queue
- Dependency Resolvers in Galaxy
- 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.xmlmethod. - 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 Reports
- Scripts & Tricks
- Configuration Options
config_dirmanaged_config_dirdata_dircache_dirdatabase_connectiondatabase_engine_option_pool_sizedatabase_engine_option_max_overflowdatabase_engine_option_pool_recycledatabase_engine_option_server_side_cursorsdatabase_query_profiling_proxydatabase_templatedatabase_log_query_countsslow_query_log_thresholdenable_per_request_sql_debugginginstall_database_connectiondatabase_auto_migratedatabase_waitdatabase_wait_attemptsdatabase_wait_sleephistory_audit_table_prune_intervalfile_pathnew_file_pathtool_config_fileshed_tool_config_filecheck_migrate_toolsmigrated_tools_configintegrated_tool_panel_configtool_pathtool_dependency_dirdependency_resolvers_config_fileconda_prefixconda_execconda_debugconda_ensure_channelsconda_use_localconda_auto_installconda_auto_initconda_copy_dependencieslocal_conda_mapping_filemodules_mapping_filesuse_cached_dependency_managertool_dependency_cache_dirprecache_dependenciestool_sheds_config_filewatch_toolswatch_job_ruleswatch_core_configwatch_toursfile_sources_config_fileenable_mulled_containerscontainer_resolvers_config_filecontainer_resolversinvolucro_pathinvolucro_auto_initmulled_channelsenable_tool_shed_checkhours_between_checktool_data_table_config_pathshed_tool_data_table_configtool_data_pathshed_tool_data_pathwatch_tool_data_dirrefgenie_config_filebuild_sites_config_filebuilds_file_pathlen_file_pathdatatypes_config_filesniff_compressed_dynamic_datatypes_defaultdatatypes_disable_autovisualization_plugins_directoryinteractive_environment_plugins_directorytour_config_dirwebhooks_dirjob_working_directorycluster_files_directorytemplate_cache_pathcheck_job_script_integritycheck_job_script_integrity_countcheck_job_script_integrity_sleepdefault_job_shellenable_tool_document_cachetool_cache_data_dirtool_search_index_dirdelay_tool_initializationbiotools_content_directorybiotools_use_apibiotools_service_cache_typebiotools_service_cache_data_dirbiotools_service_cache_lock_dircitation_cache_typecitation_cache_data_dircitation_cache_lock_dirmulled_resolution_cache_typemulled_resolution_cache_data_dirmulled_resolution_cache_lock_dirobject_store_config_fileobject_store_store_bysmtp_serversmtp_usernamesmtp_passwordsmtp_sslmailing_join_addrmailing_join_subjectmailing_join_bodyerror_email_toemail_fromcustom_activation_email_messageinstance_resource_urlemail_domain_blocklist_fileemail_domain_allowlist_fileregistration_warning_messageuser_activation_onactivation_grace_periodinactivity_box_contentpassword_expiration_periodenable_account_interfacesession_durationga_codeplausible_serverplausible_domainmatomo_servermatomo_site_iddisplay_serversenable_old_display_applicationsaws_estimateinteractivetools_enableinteractivetools_proxy_hostinteractivetools_base_pathinteractivetools_mapinteractivetools_prefixinteractivetools_shorten_urlretry_interactivetool_metadata_internallyvisualizations_visiblemessage_box_visiblemessage_box_contentmessage_box_classbranddisplay_galaxy_brandpretty_datetime_formattrs_servers_config_fileuser_preferences_extra_conf_pathdefault_localegalaxy_infrastructure_urlgalaxy_infrastructure_web_portwelcome_urllogo_urllogo_srclogo_src_secondaryhelpsite_urlwiki_urlquota_urlsupport_urlcitation_urlrelease_doc_base_urlsearch_urlmailing_lists_urlscreencasts_urlterms_urlqa_urlstatic_enabledstatic_cache_timestatic_dirstatic_images_dirstatic_favicon_dirstatic_scripts_dirstatic_style_dirstatic_robots_txtdisplay_chunk_sizeapache_xsendfilenginx_x_accel_redirect_baseupstream_gzipupstream_mod_zipx_frame_optionsnginx_upload_storenginx_upload_pathnginx_upload_job_files_storenginx_upload_job_files_pathchunk_upload_sizedynamic_proxy_managedynamic_proxydynamic_proxy_session_mapdynamic_proxy_bind_portdynamic_proxy_bind_ipdynamic_proxy_debugdynamic_proxy_external_proxydynamic_proxy_prefixdynamic_proxy_golang_noaccessdynamic_proxy_golang_clean_intervaldynamic_proxy_golang_docker_addressdynamic_proxy_golang_api_keyauto_configure_logginglog_levelloggingdatabase_engine_option_echodatabase_engine_option_echo_poollog_eventslog_actionsfluent_logfluent_hostfluent_portsanitize_all_htmlsanitize_allowlist_fileserve_xss_vulnerable_mimetypesallowed_origin_hostnamestrust_jupyter_notebook_conversiondebuguse_lintuse_profileuse_printdebugmonitor_thread_join_timeoutuse_heartbeatheartbeat_intervalheartbeat_logsentry_dsnsentry_event_levelstatsd_hoststatsd_portstatsd_prefixstatsd_influxdbstatsd_mock_callslibrary_import_diruser_library_import_diruser_library_import_dir_auto_creationuser_library_import_symlink_allowlistuser_library_import_check_permissionsallow_path_pastedisable_library_comptypestool_name_boosttool_id_boosttool_section_boosttool_description_boosttool_label_boosttool_stub_boosttool_help_boosttool_search_limittool_enable_ngram_searchtool_ngram_minsizetool_ngram_maxsizetool_test_data_directoriesid_secretuse_remote_userremote_user_maildomainremote_user_headerremote_user_secretremote_user_logout_hrefnormalize_remote_user_emailsingle_useradmin_usersrequire_loginshow_welcome_with_loginallow_user_creationallow_user_deletionallow_user_impersonationshow_user_prepopulate_formupload_from_form_buttonallow_user_dataset_purgenew_user_dataset_access_role_default_privateexpose_user_nameexpose_user_emailfetch_url_allowlistenable_beta_gdprenable_beta_containers_interfaceenable_beta_workflow_modulesedam_panel_viewsedam_toolbox_ontology_pathpanel_views_dirpanel_viewsdefault_panel_viewdefault_workflow_export_formatforce_beta_workflow_scheduled_min_stepsforce_beta_workflow_scheduled_for_collectionsparallelize_workflow_scheduling_within_historiesmaximum_workflow_invocation_durationmaximum_workflow_jobs_per_scheduling_iterationflush_per_n_datasetshistory_local_serial_workflow_schedulingenable_oidcoidc_config_fileoidc_backends_config_fileauth_config_fileapi_allow_run_asmaster_api_keyenable_openidopenid_consumer_cache_pathenable_tool_tagsenable_unique_workflow_defaultssimplified_workflow_run_uisimplified_workflow_run_ui_target_historysimplified_workflow_run_ui_job_cachemyexperiment_target_urlftp_upload_siteftp_upload_dirftp_upload_dir_identifierftp_upload_dir_templateftp_upload_purgeenable_quotasexpose_dataset_pathjob_metrics_config_fileexpose_potentially_sensitive_job_metricsenable_legacy_sample_tracking_apienable_data_manager_user_viewdata_manager_config_fileshed_data_manager_config_filegalaxy_data_manager_data_pathjob_config_filejob_configdependency_resolversdependency_resolutiondefault_job_resubmission_conditiontrack_jobs_in_databaseuse_tasked_jobslocal_task_queue_workersjob_handler_monitor_sleepjob_runner_monitor_sleepmetadata_strategyretry_metadata_internallymax_metadata_value_sizeoutputs_to_working_directoryretry_job_output_collectionpreserve_python_environmentcleanup_jobdrmaa_external_runjob_scriptdrmaa_external_killjob_scriptexternal_chown_scriptreal_system_usernameenvironment_setup_fileenable_beta_markdown_exportmarkdown_export_cssmarkdown_export_css_pagesmarkdown_export_css_invocation_reportsmarkdown_export_prologuemarkdown_export_epiloguemarkdown_export_prologue_pagesmarkdown_export_prologue_invocation_reportsmarkdown_export_epilogue_pagesmarkdown_export_epilogue_invocation_reportsjob_resource_params_fileworkflow_resource_params_fileworkflow_resource_params_mapperworkflow_schedulers_config_filecache_user_job_counttool_filterstool_label_filterstool_section_filtersuser_tool_filtersuser_tool_section_filtersuser_tool_label_filterstoolbox_filter_base_modulesamqp_internal_connectionenable_celery_tasksuse_pbkdf2cookie_domainselect_type_workflow_thresholdenable_tool_recommendationstool_recommendation_model_pathtopk_recommendationsadmin_tool_recommendations_pathoverwrite_model_recommendationserror_report_filecontainers_config_filetool_destinations_config_filewelcome_directory