Warning
This document is for an in-development version 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
- 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_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_sleepfile_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_dependenciesuse_cached_dependency_managertool_dependency_cache_dirprecache_dependenciestool_sheds_config_filewatch_toolswatch_job_ruleswatch_core_configwatch_tourslegacy_eager_objectstore_initializationenable_mulled_containerscontainers_resolvers_config_fileinvolucro_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_shelltool_cache_data_dirtool_search_index_dirdelay_tool_initializationcitation_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_addrerror_email_toemail_frominstance_resource_urlblacklist_filewhitelist_fileregistration_warning_messageuser_activation_onactivation_grace_periodinactivity_box_contentpassword_expiration_periodsession_durationga_codedisplay_serversenable_old_display_applicationsinteractivetools_enableaws_estimateinteractivetools_proxy_hostinteractivetools_mapvisualizations_visiblemessage_box_visiblemessage_box_contentmessage_box_classbranddisplay_galaxy_brandpretty_datetime_formatuser_preferences_extra_conf_pathdefault_localegalaxy_infrastructure_urlgalaxy_infrastructure_web_portwelcome_urllogo_urlhelpsite_urlwiki_urlsupport_urlcitation_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_gzipx_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_whitelist_fileserve_xss_vulnerable_mimetypesallowed_origin_hostnamestrust_jupyter_notebook_conversiondebuguse_lintuse_profileuse_printdebugmonitor_thread_join_timeoutuse_heartbeatheartbeat_intervalheartbeat_logsentry_dsnsentry_sloreq_thresholdstatsd_hoststatsd_portstatsd_prefixstatsd_influxdblibrary_import_diruser_library_import_diruser_library_import_dir_auto_creationuser_library_import_symlink_whitelistuser_library_import_check_permissionsallow_path_pastedisable_library_comptypestransfer_manager_porttool_name_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_formallow_user_dataset_purgenew_user_dataset_access_role_default_privateexpose_user_nameexpose_user_emailfetch_url_whitelistenable_beta_gdprenable_beta_containers_interfaceenable_beta_workflow_modulesdefault_workflow_export_formatforce_beta_workflow_scheduled_min_stepsforce_beta_workflow_scheduled_for_collectionsparallelize_workflow_scheduling_within_historiesmaximum_workflow_invocation_durationmaximum_workflow_jobs_per_scheduling_iterationhistory_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_defaultsmyexperiment_target_urlftp_upload_dirftp_upload_siteftp_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_workersenable_job_recoverymetadata_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_communication_servercommunication_server_hostcommunication_server_portpersistent_communication_roomsuse_pbkdf2cookie_domainselect_type_workflow_thresholdenable_tool_recommendationstool_recommendation_model_pathtopk_recommendationsadmin_tool_recommendations_pathoverwrite_model_recommendations