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galaxyservers.yml
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galaxyservers.yml
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---
## these vars are defined in the vaulted (secret) vars file
#
# used by: galaxyprojectdotorg.galaxy (templating job_conf.xml)
#galaxy_job_conf_amqp_url
#
# used by: galaxy_config var
#galaxy_config_database_connection
#galaxy_config_install_database_connection
#galaxy_config_admin_users
#galaxy_config_id_secret
#galaxy_config_biostar_key
#galaxy_config_sentry_dsn
#galaxy_config_amqp_internal_connection
## used by: other vars in this vars file
galaxy_log_dir: "{{ galaxy_root }}/log"
# instance_root and galaxy_root are set in the play
# these are the same on galaxy servers
# on pulsar servers, galaxy_root is a subdirectory of instance_root
#instance_root:
#galaxy_root:
## used by: the play itself
galaxy_user: g2main
galaxy_system_group: G-803372
# also by usegalaxy_admin
galaxy_privileged_user: gxsrc
galaxy_root: /srv/galaxy/{{ galaxy_instance_codename }}
galaxy_server_dir: "/cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/galaxy"
## used by: supervisor
galaxy_instance_codename: main
galaxy_handler_count: 3
supervisord_group_configs:
- galaxy
- galaxy_impersonate
- galaxy_reports
- galaxy_group
# supervisor template
galaxy_installer_venv_dir: "/cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/venv"
## used by: galaxyprojectdotorg.nginx
nginx_flavor: galaxy
nginx_default_redirect_uri: https://usegalaxy.org$request_uri
nginx_conf_http:
server_names_hash_bucket_size: 128
gzip_vary: 'on'
gzip_proxied: any
gzip_comp_level: 6
gzip_buffers: 16 8k
gzip_http_version: 1.1
gzip_types: text/plain text/css application/json application/x-javascript text/xml application/xml application/xml+rss text/javascript
client_max_body_size: 50g
proxy_read_timeout: 600
uwsgi_read_timeout: 300
nginx_configs:
- usegalaxy
- galaxy_bx
nginx_extra_configs:
- usegalaxy_rewrites.conf
nginx_conf_user: g2main
nginx_conf_group: G-803372
nginx_conf_worker_processes: 8
nginx_conf_ssl_certificate: "{{ nginx_conf_dir }}/ssl/usegalaxy.org_cert.pem"
nginx_conf_ssl_certificate_key: "{{ nginx_conf_dir }}/ssl/usegalaxy.org_privatekey.pem"
nginx_enable_default_ipv6: false
nginx_supervisor: true
## used by: usegalaxy, usegalaxy_static
nginx_srv: /srv/nginx
galaxy_instance_hostname: usegalaxy.org
usegalaxy_dynamic_job_rules:
- files/galaxy/{{ galaxy_instance_hostname }}/dynamic_rules/reserved.py
- files/galaxy/{{ galaxy_instance_hostname }}/dynamic_rules/multi_dynamic_walltime.py
usegalaxy_nagios_tools:
- echo_main_w1_handler0
- echo_main_w1_handler1
- echo_main_w1_handler2
- echo_main_w2_handler0
- echo_main_w2_handler1
- echo_main_w2_handler2
- echo_main_cluster
- echo_main_stampede
## used by the sysctl task in the galaxy_infrastructure playbook
sysctl_conf:
- name: net.core.rmem_max
value: 15990784
- name: net.core.wmem_max
value: 15990784
## used by: usegalaxy_admin
galaxy_log_archive_dir: /galaxy-repl/{{ galaxy_instance_codename }}/backup/log
## used by: galaxyprojectdotorg.tools
galaxy_instance_url: "{{ galaxy_instance_hostname }}"
tool_list_file: files/galaxy/usegalaxy.org/tool_list.yaml
## used by: galaxyprojectdotorg.interactive_environments
interactive_environments_install_method: copy
interactive_environments_plugins_local_path: "{{ deploy_env }}/files/interactive_environments/plugins"
interactive_environments_proxy_local_path: "{{ deploy_env }}/files/interactive_environments/proxy"
interactive_environments_plugins_path: "{{ galaxy_root }}/interactive_environments/plugins"
interactive_environments_proxy_path: "{{ galaxy_root }}/interactive_environments/proxy"
interactive_environments_enabled:
- jupyter
interactive_environments_config_files:
- ie_name: jupyter
file: jupyter.ini
contents:
docker:
command: "docker -H tcp://iedocker.galaxyproject.org:2376 --tlsverify {docker_args}"
galaxy_url: "https://usegalaxy.org"
docker_hostname: "iedocker.galaxyproject.org"
- ie_name: jupyter
file: allowed_images.yml
contents:
- image: "quay.io/bgruening/docker-jupyter-notebook:16.01.1"
description: >
The Jupyter notebook is the next iteration of IPython, allowing
analysis in many different languages. This image features the Python,
R, Julia, Haskell, Bash kernels and many scientific analysis stacks for
each.
interactive_environments_proxy_user: "{{ galaxy_user }}"
interactive_environments_access_log_path: "{{ galaxy_log_dir }}/gie_proxy-access.log"
interactive_environments_error_log_path: "{{ galaxy_log_dir }}/gie_proxy-error.log"
## used by: galaxyprojectdotorg.galaxy
pip_virtualenv_command: "{{ galaxy_root }}/python/bin/virtualenv"
# some things are always local
galaxy_venv_dir: "/cvmfs/{{ galaxy_instance_codename }}.galaxyproject.org/venv"
galaxy_config_dir: "{{ galaxy_root }}/config"
galaxy_config_file: "{{ galaxy_config_dir }}/galaxy.ini"
galaxy_mutable_config_dir: "{{ galaxy_root }}/var"
galaxy_mutable_data_dir: "{{ galaxy_root }}/var"
galaxy_admin_email_to: galaxy-lab@bx.psu.edu
base_app_main: &BASE_APP_MAIN
# message box
message_box_visible: "True"
#message_box_content: 'Galaxy will be unavailable between 12:00 PM - 6:00 PM EST (UTC -0500) <strong>today</strong>, Tuesday, November 10th due to <a target="_blank" href="https://portal.tacc.utexas.edu/user-news/-/news/101798">filesystem maintenance</a>. Running jobs may be interrupted during this period.'
message_box_content: 'We have updated Galaxy to the forthcoming 16.04 release and made some configuration and deployment changes, so you may encounter a few problems. We are working on these, and please feel free to report any errors you encounter.'
message_box_class: warning
# 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: "{{ galaxy_config_install_database_connection }}"
id_secret: "{{ galaxy_config_id_secret }}"
admin_users: "{{ galaxy_config_admin_users }}"
biostar_key: "{{ galaxy_config_biostar_key }}"
sentry_dsn: "{{ galaxy_config_sentry_dsn }}"
amqp_internal_connection: "{{ galaxy_config_amqp_internal_connection }}"
# paths
tool_config_file: "{{ galaxy_config_dir }}/tool_conf.xml,{{ galaxy_mutable_config_dir }}/shed_tool_conf.xml,{{ galaxy_config_dir }}/nagios_tool_conf.xml"
tool_dependency_dir: /galaxy/main/deps
job_working_directory: /galaxy/main/jobdir
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/main/ftp
user_library_import_dir: /galaxy/main/ftp
library_import_dir: /galaxy-repl/main/import
galaxy_data_manager_data_path: /galaxy-repl/manageddata/data
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"
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"
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"
migrated_tools_config: "{{ galaxy_mutable_config_dir }}/migrated_tools_conf.xml"
shed_tool_data_table_config: "{{ galaxy_mutable_config_dir }}/shed_tool_data_table_conf.xml"
sanitize_whitelist_file: /galaxy-repl/main/config/sanitize_whitelist.txt
#environment_setup_file: /galaxy/main/job_env.bash
builds_file_path: "{{ galaxy_config_dir }}/builds.txt"
ucsc_build_sites: "{{ galaxy_config_dir }}/ucsc_build_sites.txt"
# interactive environments
interactive_environment_plugins_directory: "{{ interactive_environments_plugins_path }}"
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: /galaxy-repl/localdata/chrom
collect_outputs_from: job_working_directory
smtp_server: localhost
error_email_to: galaxy-bugs@bx.psu.edu
activation_email: "Galaxy Activation <activate@galaxyproject.org>"
instance_resource_url: "http://wiki.galaxyproject.org/Support"
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."
wiki_url: "http://wiki.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: "False"
allow_user_deletion: "True"
allow_user_dataset_purge: "True"
enable_openid: "True"
ftp_upload_site: "{{ galaxy_instance_hostname }}"
enable_quotas: "True"
track_jobs_in_database: "True"
retry_metadata_internally: "False"
retry_job_output_collection: 5
# FIXME: reenable onsuccess after this is fixed: https://github.com/galaxyproject/pulsar/issues/111
#cleanup_job: onsuccess
cleanup_job: never
biostar_url: "https://biostar.usegalaxy.org"
biostar_key_name: biostar-login
biostar_enable_bug_reports: "False"
max_metadata_value_size: 1000000
use_heartbeat: "True"
heartbeat_interval: -1
heartbeat_log: "{{ galaxy_log_dir }}/heartbeat_{server_name}.log"
tool_search_limit: 30
tool_name_boost: 12
tool_section_boost: 5
# galaxy.ini contents
galaxy_config_hash:
"app:main":
<<: *BASE_APP_MAIN
allow_user_impersonation: "False"
new_file_path: /galaxy/main/scratch
impersonate_config_hash:
"server:main_w1_impersonate":
threadpool_workers: 5
host: 0.0.0.0
port: 9480
"server:main_w2_impersonate":
threadpool_workers: 5
host: 0.0.0.0
port: 9480
"filter:proxy-prefix":
use: "egg:PasteDeploy#prefix"
prefix: /main/impersonate
"app:main":
<<: *BASE_APP_MAIN
allow_user_impersonation: "True"
"filter-with": proxy-prefix
new_file_path: /galaxy/main/scratch
installer_config_hash:
"server:main_w1_installer":
threadpool_workers: 5
host: 0.0.0.0
port: 9999
"app:main":
<<: *BASE_APP_MAIN
allow_user_impersonation: "False"
new_file_path: /srv/galaxy/main/var/installer_tmp
datamanager_config_hash:
"app:main":
<<: *BASE_APP_MAIN
new_file_path: /galaxy-repl/main/scratch
# specifies config files to copy from the playbook
galaxy_config_files:
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/tool_data_table_conf.xml
dest: "{{ galaxy_config_dir }}/tool_data_table_conf.xml"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/tool_conf.xml
dest: "{{ galaxy_config_dir }}/tool_conf.xml"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/nagios_tool_conf.xml
dest: "{{ galaxy_config_dir }}/nagios_tool_conf.xml"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/object_store_conf.xml
dest: "{{ galaxy_config['app:main']['object_store_config_file'] }}"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/data_manager_conf.xml
dest: "{{ galaxy_config['app:main']['data_manager_config_file'] }}"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/tool_sheds_conf.xml
dest: "{{ galaxy_config['app:main']['tool_sheds_config_file'] }}"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/job_metrics_conf.xml
dest: "{{ galaxy_config['app:main']['job_metrics_config_file'] }}"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/job_resource_params_conf.xml
dest: "{{ galaxy_config['app:main']['job_resource_params_file'] }}"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/pulsar_stampede_actions.yml
dest: "{{ galaxy_config_dir }}/pulsar_stampede_actions.yml"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/pulsar_jetstream.yml
dest: "{{ galaxy_config_dir }}/pulsar_jetstream.yml"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/pulsar_jetstream_actions.yml
dest: "{{ galaxy_config_dir }}/pulsar_jetstream_actions.yml"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/builds.txt
dest: "{{ galaxy_config['app:main']['builds_file_path'] }}"
- src: files/galaxy/{{ galaxy_instance_hostname }}/config/ucsc_build_sites.txt
dest: "{{ galaxy_config['app:main']['ucsc_build_sites'] }}"
# specifies config files to template from the playbook
galaxy_config_templates:
- src: templates/galaxy/{{ galaxy_instance_hostname }}/config/job_conf.xml.j2
dest: "{{ galaxy_config_dir }}/job_conf.xml"
- src: templates/galaxy/{{ galaxy_instance_hostname }}/config/datatypes_conf.xml.j2
dest: "{{ galaxy_config['app:main']['datatypes_config_file'] }}"
- src: templates/galaxy/{{ galaxy_instance_hostname }}/config/disposable_email_blacklist.conf.j2
dest: "{{ galaxy_config['app:main']['blacklist_file'] }}"
- src: templates/galaxy/{{ galaxy_instance_hostname }}/config/reports.ini.j2
dest: "{{ galaxy_config_dir }}/reports.ini"
- src: templates/galaxy/{{ galaxy_instance_hostname }}/config/uwsgi.ini.j2
dest: "{{ galaxy_config_dir }}/uwsgi.ini"