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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.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 Reports
- Scripts & Tricks
- Configuration Options
config_dir
data_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
file_path
new_file_path
tool_config_file
shed_tool_config_file
check_migrate_tools
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
use_cached_dependency_manager
tool_dependency_cache_dir
precache_dependencies
tool_sheds_config_file
watch_tools
watch_job_rules
watch_core_config
watch_tours
legacy_eager_objectstore_initialization
enable_mulled_containers
containers_resolvers_config_file
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
build_sites_config_file
builds_file_path
len_file_path
datatypes_config_file
sniff_compressed_dynamic_datatypes_default
datatypes_disable_auto
visualization_plugins_directory
interactive_environment_plugins_directory
tour_config_dir
webhooks_dir
job_working_directory
cluster_files_directory
template_cache_path
check_job_script_integrity
check_job_script_integrity_count
check_job_script_integrity_sleep
default_job_shell
citation_cache_type
citation_cache_data_dir
citation_cache_lock_dir
mulled_resolution_cache_type
mulled_resolution_cache_data_dir
mulled_resolution_cache_lock_dir
object_store_config_file
object_store_store_by
smtp_server
smtp_username
smtp_password
smtp_ssl
mailing_join_addr
error_email_to
email_from
instance_resource_url
blacklist_file
registration_warning_message
user_activation_on
activation_grace_period
inactivity_box_content
password_expiration_period
session_duration
ga_code
display_servers
enable_old_display_applications
interactivetools_enable
interactivetools_proxy_host
interactivetools_map
visualizations_visible
message_box_visible
message_box_content
message_box_class
brand
display_galaxy_brand
pretty_datetime_format
user_preferences_extra_conf_path
default_locale
galaxy_infrastructure_url
galaxy_infrastructure_web_port
welcome_url
logo_url
helpsite_url
wiki_url
support_url
citation_url
search_url
mailing_lists_url
screencasts_url
terms_url
qa_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
x_frame_options
nginx_upload_store
nginx_upload_path
nginx_upload_job_files_store
nginx_upload_job_files_path
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_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_whitelist_file
serve_xss_vulnerable_mimetypes
allowed_origin_hostnames
trust_jupyter_notebook_conversion
debug
use_lint
use_profile
use_printdebug
monitor_thread_join_timeout
use_heartbeat
heartbeat_interval
heartbeat_log
sentry_dsn
sentry_sloreq_threshold
statsd_host
statsd_port
statsd_prefix
statsd_influxdb
library_import_dir
user_library_import_dir
user_library_import_dir_auto_creation
user_library_import_symlink_whitelist
user_library_import_check_permissions
allow_path_paste
disable_library_comptypes
transfer_manager_port
tool_name_boost
tool_section_boost
tool_description_boost
tool_label_boost
tool_stub_boost
tool_help_boost
tool_search_limit
tool_enable_ngram_search
tool_ngram_minsize
tool_ngram_maxsize
tool_test_data_directories
id_secret
use_remote_user
remote_user_maildomain
remote_user_header
remote_user_secret
remote_user_logout_href
normalize_remote_user_email
single_user
admin_users
require_login
show_welcome_with_login
allow_user_creation
allow_user_deletion
allow_user_impersonation
show_user_prepopulate_form
allow_user_dataset_purge
new_user_dataset_access_role_default_private
expose_user_name
expose_user_email
fetch_url_whitelist
enable_beta_gdpr
enable_beta_containers_interface
enable_beta_workflow_modules
default_workflow_export_format
force_beta_workflow_scheduled_min_steps
force_beta_workflow_scheduled_for_collections
parallelize_workflow_scheduling_within_histories
maximum_workflow_invocation_duration
maximum_workflow_jobs_per_scheduling_iteration
history_local_serial_workflow_scheduling
enable_oidc
oidc_config_file
oidc_backends_config_file
auth_config_file
api_allow_run_as
master_api_key
enable_openid
openid_consumer_cache_path
enable_tool_tags
enable_unique_workflow_defaults
myexperiment_target_url
ftp_upload_dir
ftp_upload_site
ftp_upload_dir_identifier
ftp_upload_dir_template
ftp_upload_purge
enable_quotas
expose_dataset_path
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
enable_job_recovery
retry_metadata_internally
max_metadata_value_size
outputs_to_working_directory
retry_job_output_collection
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
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_communication_server
communication_server_host
communication_server_port
persistent_communication_rooms
use_pbkdf2
cookie_domain
select_type_workflow_threshold