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galaxy_config_vars.yml
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galaxy_config_vars.yml
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---
## these vars are defined in vault.yml
#
# used by: galaxy_config var
galaxy_config_database_connection: "{{ vault_galaxy_config_database_connection }}"
galaxy_config_admin_users: "{{ vault_galaxy_config_admin_users }}"
galaxy_config_id_secret: "{{ vault_galaxy_config_id_secret }}"
galaxy_config_sentry_dsn: "{{ vault_galaxy_config_sentry_dsn }}"
galaxy_config_amqp_internal_connection: "{{ vault_galaxy_config_amqp_internal_connection }}"
galaxy_root: "/srv/galaxy/{{ galaxy_instance_codename }}"
galaxy_new_file_path: "/galaxy-repl/{{ galaxy_instance_codename }}/scratch2"
galaxy_job_working_directory: "/galaxy-repl/{{ galaxy_instance_codename }}/jobdir"
galaxy_ftp_upload_dir: "/galaxy-repl/{{ galaxy_instance_codename }}/ftp"
galaxy_tool_dependency_dir: "/galaxy/{{ galaxy_instance_codename }}/deps"
galaxy_file_path: "{{ galaxy_mutable_data_dir }}/datasets"
galaxy_log_dir: "{{ galaxy_root }}/log"
galaxy_tool_cache_data_dir: "/srv/galaxy/{{ galaxy_instance_codename }}/var/tool_cache"
galaxy_tool_search_index_dir: "/srv/galaxy/{{ galaxy_instance_codename }}/var/tool_search_index"
# for future use
#galaxy_object_store_cache_path: "/galaxy-repl/{{ galaxy_instance_codename }}/object_store_cache"
## used by: galaxyproject.galaxy
base_app_main: &BASE_APP_MAIN
# message box
#message_box_visible: "True"
#message_box_class: info
#message_box_class: warning
#message_box_class: error
# informational messages
#message_box_content: Galaxy has recently been upgraded to a pre-release of the next Galaxy stable release (18.05). Please report any issues you encounter using the bug icon on error (red) datasets, or email <a href="mailto:galaxy-bugs@galaxyproject.org">galaxy-bugs</a>.
# emergency downtimes
#message_box_content: Certain large memory tools are not functioning due to issues with the Bridges supercomputer at PSC. Affected tools include Trinity, SPAdes, Unicycler, and RNA STAR.
#message_box_content: All tools should be functioning normally with the exception of RNA STAR.
#message_box_content: Jobs are currently paused due to unexpected filesystem issues. We are working on the issue and jobs will be resumed as soon as possible.
# scheduled downtimes
#message_box_content: Galaxy will be down for four hours beginning at <a target="_blank" href="https://www.timeanddate.com/worldclock/fixedtime.html?iso=20200618T090000&p1=24&ah=">2:00 PM UTC, Thursday, June 18</a> for database server upgrades
#message_box_content: Cluster upgrades are in progress, jobs will not run until upgrades are complete (by <a target="_blank" href="https://www.timeanddate.com/worldclock/fixedtime.html?iso=20180417T160000&p1=24&ah=">9:00 PM UTC, Tuesday, April 17</a>).
# this can be removed after 9/22 and the datatypes_conf.xml update
gbrowse_display_sites: wormbase,tair,modencode_worm,modencode_fly
ucsc_display_sites: main,archaea,ucla
# secrets
database_connection: "{{ galaxy_config_database_connection }}"
install_database_connection: "sqlite:////cvmfs/main.galaxyproject.org/var/galaxy_main_install.sqlite?isolation_level=IMMEDIATE"
id_secret: "{{ galaxy_config_id_secret }}"
admin_users: "{{ galaxy_config_admin_users }}"
sentry_dsn: "{{ galaxy_config_sentry_dsn }}"
sentry_sloreq_threshold: 10.0
amqp_internal_connection: "{{ galaxy_config_amqp_internal_connection }}"
# paths
tool_config_file: "{{ galaxy_config_dir }}/tool_conf.xml,{{ galaxy_shed_tool_conf_file }},{{ galaxy_config_dir }}/nagios_tool_conf.xml"
tool_dependency_dir: "{{ galaxy_tool_dependency_dir }}"
job_working_directory: "{{ galaxy_job_working_directory }}"
tool_data_path: /galaxy-repl/main/tool_data
nginx_upload_store: /galaxy-repl/main/upload
nginx_upload_job_files_store: /galaxy-repl/main/upload_job_files
ftp_upload_dir: "{{ galaxy_ftp_upload_dir }}"
user_library_import_dir: /galaxy-repl/main/ftp
library_import_dir: /galaxy-repl/main/import
galaxy_data_manager_data_path: /galaxy-repl/manageddata/data
tool_cache_data_dir: "{{ galaxy_tool_cache_data_dir }}"
tool_search_index_dir: "{{ galaxy_tool_search_index_dir }}"
tool_sheds_config_file: "{{ galaxy_config_dir }}/tool_sheds_conf.xml"
tool_data_table_config_path: "{{ galaxy_config_dir }}/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml"
build_sites_config_file: "{{ galaxy_config_dir }}/build_sites.yml"
#datatypes_config_file: "{{ galaxy_config_dir }}/datatypes_conf.xml"
object_store_config_file: "{{ galaxy_config_dir }}/object_store_conf.xml"
job_config_file: "{{ galaxy_config_dir }}/job_conf.xml"
workflow_schedulers_config_file: "{{ galaxy_config_dir }}/workflow_schedulers_conf.xml"
job_resource_params_file: "{{ galaxy_config_dir }}/job_resource_params_conf.xml"
data_manager_config_file: "{{ galaxy_config_dir }}/data_manager_conf.xml"
job_metrics_config_file: "{{ galaxy_config_dir }}/job_metrics_conf.xml"
dependency_resolvers_config_file: "{{ galaxy_config_dir }}/dependency_resolvers_conf.xml"
migrated_tools_config: "/cvmfs/main.galaxyproject.org/config/migrated_tools_conf.xml"
shed_tool_data_table_config: "/cvmfs/main.galaxyproject.org/config/shed_tool_data_table_conf.xml"
shed_data_manager_config_file: "/cvmfs/main.galaxyproject.org/config/shed_data_manager_conf.xml"
integrated_tool_panel_config: "{{ galaxy_mutable_config_dir }}/integrated_tool_panel.xml"
sanitize_whitelist_file: /galaxy-repl/main/config/sanitize_whitelist.txt
containers_config_file: "{{ galaxy_config_dir }}/containers.yml"
enable_beta_containers_interface: "True"
#environment_setup_file: /galaxy/main/job_env.bash
builds_file_path: "/cvmfs/data.galaxyproject.org/managed/location/builds.txt"
ucsc_build_sites: "/cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt"
# interactive environments
interactive_environment_plugins_directory: "{{ galaxy_root }}/interactive_environments/plugins"
dynamic_proxy_manage: "False"
dynamic_proxy_session_map: /srv/galaxy/main/var/gie_proxy_session_map.sqlite
dynamic_proxy_bind_port: 4280
dynamic_proxy_bind_ip: 0.0.0.0
dynamic_proxy_debug: "True"
dynamic_proxy_external_proxy: "True"
dynamic_proxy_prefix: gie_proxy
galaxy_infrastructure_url: https://usegalaxy.org
#trust_ipython_notebook_conversion: "True"
# general stuff
database_engine_option_pool_size: 10
database_engine_option_max_overflow: 20
database_engine_option_server_side_cursors: "True"
manage_dependency_relationships: "False"
len_file_path: /cvmfs/data.galaxyproject.org/managed/len/ucsc
collect_outputs_from: job_working_directory
smtp_server: localhost
error_email_to: galaxy-bugs@galaxyproject.org
activation_email: "Galaxy Activation <activate@galaxyproject.org>"
instance_resource_url: "https://galaxyproject.org/support"
screencasts_url: "https://vimeo.com/galaxyproject"
search_url: "https://galaxyproject.org/search/"
blacklist_file: "{{ galaxy_config_dir }}/disposable_email_blacklist.conf"
registration_warning_message: "Please register only one account. The {{ galaxy_instance_hostname }} service is provided free of charge and has limited computational and data storage resources. <strong>Registration and usage of multiple accounts is tracked and such accounts are subject to termination and data deletion.</strong>"
user_activation_on: "True"
activation_grace_period: 6
inactivity_box_content: "Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address."
helpsite_url: "https://help.galaxyproject.org/"
wiki_url: "https://galaxyproject.org/"
terms_url: "https://{{ galaxy_instance_hostname }}/static/terms.html"
ga_code: "UA-45719423-10"
static_enabled: "True"
enable_cloud_launch: "True"
cloudlaunch_default_ami: ami-a7dbf6ce
nginx_x_accel_redirect_base: /_x_accel_redirect
nginx_upload_path: /_upload
nginx_upload_job_files_path: /_job_files
log_events: "False"
log_actions: "False"
debug: "False"
use_interactive: "False"
use_pbkdf2: "True"
allow_user_deletion: "True"
allow_user_dataset_purge: "True"
enable_openid: "True"
ftp_upload_site: "ftp://{{ galaxy_instance_hostname }}"
enable_quotas: "True"
track_jobs_in_database: "True"
retry_metadata_internally: "False"
retry_job_output_collection: 5
cleanup_job: onsuccess
monitor_thread_join_timeout: 60
cache_user_job_count: "True"
max_metadata_value_size: 1000000
tool_search_limit: 30
tool_name_boost: 12
tool_section_boost: 5
conda_prefix: "/cvmfs/main.galaxyproject.org/deps/_conda"
mulled_resolution_cache_data_dir: "{{ galaxy_mutable_data_dir }}/mulled/data"
mulled_resolution_cache_lock_dir: "{{ galaxy_mutable_data_dir }}/mulled/lock"
# For handler heartbeats
use_heartbeat: "True"
heartbeat_interval: "-1"
heartbeat_log: "{{ galaxy_log_dir }}/heartbeat_{server_name}_{pid}.log"
# stats
statsd_host: "127.0.0.1"
statsd_port: "8125"
statsd_prefix: "main"
# start high, decrease when we've fixed things
slow_query_log_threshold: "2"
legacy_eager_objectstore_initialization: "False"
# galaxy.yml contents
galaxy_config_hash:
uwsgi:
# basic settings
- master: true
- processes: "{{ galaxy_uwsgi_processes | default(8) }}"
- threads: 4
# uwsgi performance/robustness features
- single-interpreter: true
- thunder-lock: true
- harakiri: 600
- buffer-size: 16384
# logging
- log-maxsize: 134217728
- log-master-bufsize: 15865856
# application
- pythonpath: lib
- module: galaxy.webapps.galaxy.buildapp:uwsgi_app_factory()
# zerg mode
- master-fifo:
# fifo '0'
- "{{ galaxy_mutable_data_dir }}/zerg-new.fifo"
# fifo '1'
- "{{ galaxy_mutable_data_dir }}/zerg-run.fifo"
# fifo '2'
- "{{ galaxy_mutable_data_dir }}/zerg-old.fifo"
# attach to zerg
- zerg: "{{ galaxy_mutable_data_dir }}/zergpool.sock"
# signal the currently running instance to release the running fifo and terminate
- if-exists:
- "{{ galaxy_mutable_data_dir }}/zerg-run.fifo"
- hook-accepting1-once: writefifo:{{ galaxy_mutable_data_dir }}/zerg-run.fifo 2q
# force this instance to became the running one (slot 1)
- hook-accepting1-once: spinningfifo:{{ galaxy_mutable_data_dir }}/zerg-new.fifo 1
galaxy:
<<: *BASE_APP_MAIN
allow_user_impersonation: "False"
new_file_path: "{{ galaxy_new_file_path }}"
impersonate_config_hash:
uwsgi:
- http: :9480
- master: true
- processes: 1
- threads: 2
- offload-threads: 2
- buffer-size: 16384
- pythonpath: lib
- mount: /main/impersonate=galaxy.webapps.galaxy.buildapp:uwsgi_app()
- manage-script-name: true
galaxy:
<<: *BASE_APP_MAIN
allow_user_impersonation: "True"
new_file_path: "{{ galaxy_new_file_path }}"