Commit 3c21f6d7 authored by Chabrier Patrick's avatar Chabrier Patrick Committed by Chabrier Patrick
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config: add galaxy.yml

parent f185e861
# Galaxy is configured by default to be usable in a single-user development
# environment. To tune the application for a multi-user production
# environment, see the documentation at:
#
# http://usegalaxy.org/production
#
# Throughout this sample configuration file, except where stated otherwise,
# uncommented values override the default if left unset, whereas commented
# values are set to the default value. Relative paths are relative to the root
# Galaxy directory.
#
# Examples of many of these options are explained in more detail in the Galaxy
# Community Hub.
#
# https://galaxyproject.org/admin/config
#
# Config hackers are encouraged to check there before asking for help.
#
uwsgi:
# The address and port on which to listen. By default, only listen to
# localhost (galaxy will not be accessible over the network). Use
# ':8080' to listen on all available network interfaces.
http: 0.0.0.0:8080
# By default uWSGI allocates a very small buffer (4096 bytes) for the
# headers of each request. If you start receiving "invalid request
# block size" in your logs, it could mean you need a bigger buffer. We
# recommend at least 16384.
buffer-size: 16384
# Number of web server (worker) processes to fork after the
# application has loaded. If this is set to greater than 1, thunder-
# lock likely should be enabled below.
processes: 1
# Number of threads for each web server process.
threads: 4
# Number of threads for serving static content and handling internal
# routing requests.
offload-threads: 2
# Mapping to serve style content.
static-map: /static/style=static/style/blue
# Mapping to serve the remainder of the static content.
static-map: /static=static
# Enable the master process manager. Disabled by default for maximum
# compatibility with CTRL+C, but should be enabled for use with
# --daemon and/or production deployments.
master: false
# Path to the application's Python virtual environment. If using Conda
# for Galaxy's framework dependencies (not tools!), do not set this.
virtualenv: .venv
# Path to the application's Python library.
pythonpath: lib
# The entry point which returns the web application (e.g. Galaxy,
# Reports, etc.) that you are loading.
module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
# It is usually a good idea to set this to ``true`` if processes is
# greater than 1.
thunder-lock: false
# Cause uWSGI to respect the traditional behavior of dying on SIGTERM
# (its default is to brutally reload workers)
die-on-term: true
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGINT (its default is to brutally kill workers)
hook-master-start: unix_signal:2 gracefully_kill_them_all
# Cause uWSGI to gracefully reload workers and mules upon receipt of
# SIGTERM (its default is to brutally kill workers)
hook-master-start: unix_signal:15 gracefully_kill_them_all
# Feature necessary for proper mule signal handling
py-call-osafterfork: true
# Ensure application threads will run if `threads` is unset.
enable-threads: true
galaxy:
# If running behind a proxy server and Galaxy is served from a
# subdirectory, enable the proxy-prefix filter and set the prefix in
# the [filter:proxy-prefix] section above.
#filter-with: proxy-prefix
# If proxy-prefix is enabled and you're running more than one Galaxy
# instance behind one hostname, you will want to set this to the same
# path as the prefix in the filter above. This value becomes the
# "path" attribute set in the cookie so the cookies from each instance
# will not clobber each other.
#cookie_path: null
# By default, Galaxy uses a SQLite database at
# 'database/universe.sqlite'. You may use a SQLAlchemy connection
# string to specify an external database instead. This string takes
# many options which are explained in detail in the config file
# documentation.
#database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
# If the server logs errors about not having enough database pool
# connections, you will want to increase these values, or consider
# running more Galaxy processes.
#database_engine_option_pool_size: 5
# If the server logs errors about not having enough database pool
# connections, you will want to increase these values, or consider
# running more Galaxy processes.
#database_engine_option_max_overflow: 10
# If using MySQL and the server logs the error "MySQL server has gone
# away", you will want to set this to some positive value (7200 should
# work).
#database_engine_option_pool_recycle: -1
# If large database query results are causing memory or response time
# issues in the Galaxy process, leave the result on the server
# instead. This option is only available for PostgreSQL and is highly
# recommended.
#database_engine_option_server_side_cursors: false
# Log all database transactions, can be useful for debugging and
# performance profiling. Logging is done via Python's 'logging'
# module under the qualname
# 'galaxy.model.orm.logging_connection_proxy'
#database_query_profiling_proxy: false
# If auto-creating a postgres database on startup - it can be based on
# an existing template database. This will set that. This is probably
# only useful for testing but documentation is included here for
# completeness.
#database_template: null
# Slow query logging. Queries slower than the threshold indicated
# below will be logged to debug. A value of '0' is disabled. For
# example, you would set this to .005 to log all queries taking longer
# than 5 milliseconds.
#slow_query_log_threshold: 0
# Enable's a per request sql debugging option. If this is set to true,
# append ?sql_debug=1 to web request URLs to enable detailed logging
# on the backend of SQL queries generated during that request. This is
# useful for debugging slow endpoints during development.
#enable_per_request_sql_debugging: false
# By default, Galaxy will use the same database to track user data and
# tool shed install data. There are many situations in which it is
# valuable to separate these - for instance bootstrapping fresh Galaxy
# instances with pretested installs. The following option can be used
# to separate the tool shed install database (all other options listed
# above but prefixed with install_ are also available).
#install_database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
# Setting the following option to true will cause Galaxy to
# automatically migrate the database forward after updates. This is
# not recommended for production use.
#database_auto_migrate: false
# Dataset files are stored in this directory.
#file_path: database/files
# Temporary files are stored in this directory.
#new_file_path: database/tmp
# Tool config files, defines what tools are available in Galaxy. Tools
# can be locally developed or installed from Galaxy tool sheds.
# (config/tool_conf.xml.sample will be used if left unset and
# config/tool_conf.xml does not exist).
#tool_config_file: 'config/tool_conf.xml,config/shed_tool_conf.xml'
# Enable / disable checking if any tools defined in the above non-shed
# tool_config_files (i.e., tool_conf.xml) have been migrated from the
# Galaxy code distribution to the Tool Shed. This setting should
# generally be set to False only for development Galaxy environments
# that are often rebuilt from scratch where migrated tools do not need
# to be available in the Galaxy tool panel. If the following setting
# remains commented, the default setting will be True.
#check_migrate_tools: true
# Tool config maintained by tool migration scripts. If you use the
# migration scripts to install tools that have been migrated to the
# tool shed upon a new release, they will be added to this tool config
# file.
#migrated_tools_config: config/migrated_tools_conf.xml
# File that contains the XML section and tool tags from all tool panel
# config files integrated into a single file that defines the tool
# panel layout. This file can be changed by the Galaxy administrator
# to alter the layout of the tool panel. If not present, Galaxy will
# create it.
#integrated_tool_panel_config: integrated_tool_panel.xml
# Default path to the directory containing the tools defined in
# tool_conf.xml. Other tool config files must include the tool_path as
# an attribute in the <toolbox> tag.
#tool_path: tools
# Path to the directory in which tool dependencies are placed. This
# is used by the Tool Shed to install dependencies and can also be
# used by administrators to manually install or link to dependencies.
# For details, see: https://galaxyproject.org/admin/config/tool-
# dependencies Set the string to None to explicitly disable tool
# dependency handling. If this option is set to none or an invalid
# path, installing tools with dependencies from the Tool Shed will
# fail.
#tool_dependency_dir: database/dependencies
# The dependency resolvers config file specifies an ordering and
# options for how Galaxy resolves tool dependencies (requirement tags
# in Tool XML). The default ordering is to the use the Tool Shed for
# tools installed that way, use local Galaxy packages, and then use
# Conda if available. See https://github.com/galaxyproject/galaxy/blob
# /dev/doc/source/admin/dependency_resolvers.rst for more information
# on these options.
#dependency_resolvers_config_file: config/dependency_resolvers_conf.xml
# conda_prefix is the location on the filesystem where Conda packages
# and environments are installed IMPORTANT: Due to a current
# limitation in conda, the total length of the conda_prefix and the
# job_working_directory path should be less than 50 characters!
#conda_prefix: <tool_dependency_dir>/_conda
# Override the Conda executable to use, it will default to the one on
# the PATH (if available) and then to <conda_prefix>/bin/conda
#conda_exec: null
# Pass debug flag to conda commands.
#conda_debug: false
# conda channels to enable by default (http://conda.pydata.org/docs
# /custom-channels.html)
#conda_ensure_channels: 'iuc,bioconda,conda-forge,defaults'
# Set to True to instruct Galaxy to look for and install missing tool
# dependencies before each job runs.
#conda_auto_install: false
# Set to True to instruct Galaxy to install Conda from the web
# automatically if it cannot find a local copy and conda_exec is not
# configured.
#conda_auto_init: true
# You must set this to True if conda_prefix and job_working_directory
# are not on the same volume, or some conda dependencies will fail to
# execute at job runtime. Conda will copy packages content instead of
# creating hardlinks or symlinks. This will prevent problems with some
# specific packages (perl, R), at the cost of extra disk space usage
# and extra time spent copying packages.
#conda_copy_dependencies: false
# Certain dependency resolvers (namely Conda) take a considerable
# amount of time to build an isolated job environment in the
# job_working_directory if the job working directory is on a network
# share. Set the following option to True to cache the dependencies
# in a folder. This option is beta and should only be used if you
# experience long waiting times before a job is actually submitted to
# your cluster.
#use_cached_dependency_manager: false
# By default the tool_dependency_cache_dir is the _cache directory of
# the tool dependency directory
#tool_dependency_cache_dir: <tool_dependency_dir>/_cache
# By default, when using a cached dependency manager, the dependencies
# are cached when installing new tools and when using tools for the
# first time. Set this to False if you prefer dependencies to be
# cached only when installing new tools.
#precache_dependencies: true
# File containing the Galaxy Tool Sheds that should be made available
# to install from in the admin interface (.sample used if default does
# not exist).
#tool_sheds_config_file: config/tool_sheds_conf.xml
# Set to True to enable monitoring of tools and tool directories
# listed in any tool config file specified in tool_config_file option.
# If changes are found, tools are automatically reloaded. Watchdog (
# https://pypi.python.org/pypi/watchdog ) must be installed and
# available to Galaxy to use this option. Other options include 'auto'
# which will attempt to watch tools if the watchdog library is
# available but won't fail to load Galaxy if it is not and 'polling'
# which will use a less efficient monitoring scheme that may work in
# wider range of scenarios than the watchdog default.
#watch_tools: false
# Enable Galaxy to fetch Docker containers registered with quay.io
# generated from tool requirements resolved through conda. These
# containers (when available) have been generated using mulled -
# https://github.com/mulled. These containers are highly beta and
# availability will vary by tool. This option will additionally only
# be used for job destinations with Docker enabled.
#enable_beta_mulled_containers: false
# Container resolvers configuration (beta). Setup a file describing
# container resolvers to use when discovering containers for Galaxy.
# If this is set to None, the default containers loaded is determined
# by enable_beta_mulled_containers.
#containers_resolvers_config_file: null
# involucro is a tool used to build Docker containers for tools from
# Conda dependencies referenced in tools as `requirement`s. The
# following path is the location of involucro on the Galaxy host. This
# is ignored if the relevant container resolver isn't enabled, and
# will install on demand unless involucro_auto_init is set to False.
#involucro_path: database/dependencies/involucro
# Install involucro as needed to build Docker containers for tools.
# Ignored if relevant container resolver is not used.
#involucro_auto_init: true
# Enable automatic polling of relative tool sheds to see if any
# updates are available for installed repositories. Ideally only one
# Galaxy server process should be able to check for repository
# updates. The setting for hours_between_check should be an integer
# between 1 and 24.
#enable_tool_shed_check: false
# Enable automatic polling of relative tool sheds to see if any
# updates are available for installed repositories. Ideally only one
# Galaxy server process should be able to check for repository
# updates. The setting for hours_between_check should be an integer
# between 1 and 24.
#hours_between_check: 12
# Enable use of an in-memory registry with bi-directional
# relationships between repositories (i.e., in addition to lists of
# dependencies for a repository, keep an in-memory registry of
# dependent items for each repository.
#manage_dependency_relationships: false
# XML config file that contains data table entries for the
# ToolDataTableManager. This file is manually # maintained by the
# Galaxy administrator (.sample used if default does not exist).
#tool_data_table_config_path: config/tool_data_table_conf.xml
# XML config file that contains additional data table entries for the
# ToolDataTableManager. This file is automatically generated based on
# the current installed tool shed repositories that contain valid
# tool_data_table_conf.xml.sample files. At the time of installation,
# these entries are automatically added to the following file, which
# is parsed and applied to the ToolDataTableManager at server start
# up.
#shed_tool_data_table_config: config/shed_tool_data_table_conf.xml
# Directory where data used by tools is located. See the samples in
# that directory and the Galaxy Community Hub for help:
# https://galaxyproject.org/admin/data-integration
#tool_data_path: tool-data
# Directory where Tool Data Table related files will be placed when
# installed from a ToolShed. Defaults to tool_data_path.
#shed_tool_data_path: tool-data
# Set to True to enable monitoring of the tool_data and
# shed_tool_data_path directories. If changes in tool data table files
# are found, the tool data tables for that data manager are
# automatically reloaded. Watchdog (
# https://pypi.python.org/pypi/watchdog ) must be installed and
# available to Galaxy to use this option. Other options include 'auto'
# which will attempt to use the watchdog library if it is available
# but won't fail to load Galaxy if it is not and 'polling' which will
# use a less efficient monitoring scheme that may work in wider range
# of scenarios than the watchdog default.
#watch_tool_data_dir: false
# File containing old-style genome builds
#builds_file_path: tool-data/shared/ucsc/builds.txt
# Directory where chrom len files are kept, currently mainly used by
# trackster
#len_file_path: tool-data/shared/ucsc/chrom
# Datatypes config file(s), defines what data (file) types are
# available in Galaxy (.sample is used if default does not exist). If
# a datatype appears in multiple files, the last definition is used
# (though the first sniffer is used so limit sniffer definitions to
# one file).
#datatypes_config_file: config/datatypes_conf.xml
# Disable the 'Auto-detect' option for file uploads
#datatypes_disable_auto: false
# Visualizations config directory: where to look for individual
# visualization plugins. The path is relative to the Galaxy root dir.
# To use an absolute path begin the path with '/'. This is a comma
# separated list. Defaults to "config/plugins/visualizations".
#visualization_plugins_directory: config/plugins/visualizations
# Interactive environment plugins root directory: where to look for
# interactive environment plugins. By default none will be loaded.
# Set to config/plugins/interactive_environments to load Galaxy's
# stock plugins. These will require Docker to be configured and have
# security considerations, so proceed with caution. The path is
# relative to the Galaxy root dir. To use an absolute path begin the
# path with '/'. This is a comma separated list.
#interactive_environment_plugins_directory: null
# To run interactive environment containers in Docker Swarm mode (on
# an existing swarm), set this option to True and set
# `docker_connect_port` in the IE plugin config (ini) file(s) of any
# IE plugins you have enabled and ensure that you are not using any
# `docker run`-specific options in your plugins' `command_inject`
# options (swarm mode services run using `docker service create`,
# which has a different and more limited set of options). This option
# can be overridden on a per-plugin basis by using the `swarm_mode`
# option in the plugin's ini config file.
#interactive_environment_swarm_mode: false
# Galaxy can run a "swarm manager" service that will monitor
# utilization of the swarm and provision/deprovision worker nodes as
# necessary. The service has its own configuration file.
#swarm_manager_config_file: config/swarm_manager_conf.yml
# Interactive tour directory: where to store interactive tour
# definition files. Galaxy ships with several basic interface tours
# enabled, though a different directory with custom tours can be
# specified here. The path is relative to the Galaxy root dir. To use
# an absolute path begin the path with '/'. This is a comma separated
# list.
#tour_config_dir: config/plugins/tours
# Webhooks directory: where to store webhooks - plugins to extend the
# Galaxy UI. By default none will be loaded. Set to
# config/plugins/webhooks/demo to load Galaxy's demo webhooks. To use
# an absolute path begin the path with '/'. This is a comma separated
# list. Add test/functional/webhooks to this list to include the demo
# webhooks used to test the webhook framework.
#webhooks_dir: config/plugins/webhooks
# Each job is given a unique empty directory as its current working
# directory. This option defines in what parent directory those
# directories will be created.
#job_working_directory: database/jobs_directory
# If using a cluster, Galaxy will write job scripts and stdout/stderr
# to this directory.
#cluster_files_directory: database/pbs
# Mako templates are compiled as needed and cached for reuse, this
# directory is used for the cache
#template_cache_path: database/compiled_templates
# Set to false to disable various checks Galaxy will do to ensure it
# can run job scripts before attempting to execute or submit them.
#check_job_script_integrity: true
# Number of checks to execute if check_job_script_integrity is
# enabled.
#check_job_script_integrity_count: 35
# Time to sleep between checks if check_job_script_integrity is
# enabled (in seconds).
#check_job_script_integrity_sleep: 0.25
# Set the default shell used by non-containerized jobs Galaxy-wide.
# This defaults to bash for all jobs and can be overridden at the
# destination level for heterogeneous clusters. conda job resolution
# requires bash or zsh so if this is switched to /bin/sh for instance
# - conda resolution should be disabled. Containerized jobs always use
# /bin/sh - so more maximum portability tool authors should assume
# generated commands run in sh.
#default_job_shell: /bin/bash
# Citation related caching. Tool citations information maybe fetched
# from external sources such as http://dx.doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
#citation_cache_type: file
# Citation related caching. Tool citations information maybe fetched
# from external sources such as http://dx.doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
#citation_cache_data_dir: database/citations/data
# Citation related caching. Tool citations information maybe fetched
# from external sources such as http://dx.doi.org/ by Galaxy - the
# following parameters can be used to control the caching used to
# store this information.
#citation_cache_lock_dir: database/citations/lock
# Tools with a number of outputs not known until runtime can write
# these outputs to a directory for collection by Galaxy when the job
# is done. Previously, this directory was new_file_path, but using one
# global directory can cause performance problems, so using
# job_working_directory ('.' or cwd when a job is run) is encouraged.
# By default, both are checked to avoid breaking existing tools.
#collect_outputs_from: 'new_file_path,job_working_directory'
# Configuration file for the object store If this is set and exists,
# it overrides any other objectstore settings.
#object_store_config_file: config/object_store_conf.xml
# Galaxy sends mail for various things: subscribing users to the
# mailing list if they request it, password resets, reporting dataset
# errors, and sending activation emails. To do this, it needs to send
# mail through an SMTP server, which you may define here (host:port).
# Galaxy will automatically try STARTTLS but will continue upon
# failure.
#smtp_server: null
# If your SMTP server requires a username and password, you can
# provide them here (password in cleartext here, but if your server
# supports STARTTLS it will be sent over the network encrypted).
#smtp_username: null
# If your SMTP server requires a username and password, you can
# provide them here (password in cleartext here, but if your server
# supports STARTTLS it will be sent over the network encrypted).
#smtp_password: null
# If your SMTP server requires SSL from the beginning of the
# connection
#smtp_ssl: false
# On the user registration form, users may choose to join a mailing
# list. This is the address used to subscribe to the list. Uncomment
# and leave empty if you want to remove this option from the user
# registration form.
#mailing_join_addr: galaxy-announce-join@bx.psu.edu
# Datasets in an error state include a link to report the error.
# Those reports will be sent to this address. Error reports are
# disabled if no address is set. Also this email is shown as a
# contact to user in case of Galaxy misconfiguration and other events
# user may encounter.
#error_email_to: null
# Email address to use in the 'From' field when sending emails for
# account activations, workflow step notifications and password
# resets. We recommend using string in the following format: Galaxy
# Project <galaxy-no-reply@example.com> If not configured, '<galaxy-
# no-reply@HOSTNAME>' will be used.
#email_from: null
# URL of the support resource for the galaxy instance. Used in
# activation emails.
#instance_resource_url: 'https://galaxyproject.org/'
# E-mail domains blacklist is used for filtering out users that are
# using disposable email address during the registration. If their
# address domain matches any domain in the blacklist, they are refused
# the registration.
#blacklist_file: config/disposable_email_blacklist.conf
# Registration warning message is used to discourage people from
# registering multiple accounts. Applies mostly for the main Galaxy
# instance. If no message specified the warning box will not be shown.
#registration_warning_message: Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion.
# User account activation feature global flag. If set to "False", the
# rest of the Account activation configuration is ignored and user
# activation is disabled (i.e. accounts are active since
# registration). The activation is also not working in case the SMTP
# server is not defined.
#user_activation_on: false
# Activation grace period (in hours). Activation is not forced (login
# is not disabled) until grace period has passed. Users under grace
# period can't run jobs. Enter 0 to disable grace period. Users with
# OpenID logins have grace period forever.
#activation_grace_period: 3
# Shown in warning box to users that were not activated yet. In use
# only if activation_grace_period is set.
#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.'
# Password expiration period (in days). Users are required to change
# their password every x days. Users will be redirected to the change
# password screen when they log in after their password expires. Enter
# 0 to disable password expiration.
#password_expiration_period: 0
# Galaxy Session Timeout This provides a timeout (in minutes) after
# which a user will have to log back in. A duration of 0 disables this
# feature.
#session_duration: 0
# You can enter tracking code here to track visitor's behavior through
# your Google Analytics account. Example: UA-XXXXXXXX-Y
#ga_code: null
# Galaxy can display data at various external browsers. These options
# specify which browsers should be available. URLs and builds
# available at these browsers are defined in the specifield files. If
# use_remote_user = True, display application servers will be denied
# access to Galaxy and so displaying datasets in these sites will
# fail. display_servers contains a list of hostnames which should be
# allowed to bypass security to display datasets. Please be aware
# that there are security implications if this is allowed. More
# details (including required changes to the proxy server config) are
# available in the Apache proxy documentation on the Galaxy Community
# Hub. The list of servers in this sample config are for the UCSC
# Main, Test and Archaea browsers, but the default if left commented
# is to not allow any display sites to bypass security (you must
# uncomment the line below to allow them).
#display_servers: 'hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu'
# To disable the old-style display applications that are hardcoded
# into datatype classes, set enable_old_display_applications = False.
# This may be desirable due to using the new-style, XML-defined,
# display applications that have been defined for many of the
# datatypes that have the old-style. There is also a potential
# security concern with the old-style applications, where a malicious
# party could provide a link that appears to reference the Galaxy
# server, but contains a redirect to a third-party server, tricking a
# Galaxy user to access said site.
#enable_old_display_applications: true
# Show a message box under the masthead.
#message_box_visible: false
# Show a message box under the masthead.
#message_box_content: null
# Show a message box under the masthead.
#message_box_class: info
# Append "/{brand}" to the "Galaxy" text in the masthead.
#brand: null
# Format string used when showing date and time information. The
# string may contain: - the directives used by Python time.strftime()
# function (see
# https://docs.python.org/2/library/time.html#time.strftime ), -
# $locale (complete format string for the server locale), - $iso8601
# (complete format string as specified by ISO 8601 international
# standard).
#pretty_datetime_format: $locale (UTC)
# Default localization for Galaxy UI. Allowed values are listed at the
# end of client/galaxy/scripts/nls/locale.js. With the default value
# (auto), the locale will be automatically adjusted to the user's
# navigator language. Users can override this settings in their user
# preferences if the localization settings are enabled in
# user_preferences_extra_conf.yml
#default_locale: auto
# URL (with schema http/https) of the Galaxy instance as accessible
# within your local network - if specified used as a default by pulsar