Whitespace fixes. 80 character limit. Small rewordings.

This commit is contained in:
Nicola Soranzo
2015-01-29 14:47:47 +00:00
parent c4fb70d945
commit 8d669857d5
+134 -107
View File
@@ -8,7 +8,7 @@
# 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
# 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 wiki:
@@ -118,10 +118,10 @@ paste.app_factory = galaxy.web.buildapp:app_factory
#database_query_profiling_proxy = False
# By default, Galaxy will use the same database to track user data and
# tool shed install data. There are many situtations in which it is
# tool shed install data. There are many situtations in which it is
# valuable to seperate these - for instance bootstrapping fresh Galaxy
# instances with pretested installs. The following optin can be used to
# separate the tool shed install database (all other options listed above
# instances with pretested installs. The following optin 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
@@ -139,14 +139,16 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# 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.
# 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
# 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
@@ -154,11 +156,12 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# 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.
# 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.
# 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
@@ -181,26 +184,28 @@ paste.app_factory = galaxy.web.buildapp:app_factory
#watch_tools = False
# Enable automatic polling of relative tool sheds to see if any updates
# are available for installed repositories. Ideally only one Galaxy
# 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
#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.
# 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
# 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.
# 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
@@ -215,24 +220,26 @@ paste.app_factory = galaxy.web.buildapp:app_factory
#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
# 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".
# 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 (currently just IPython). These will require Docker
# to be configured and have security considerations so proceed with caution.
#interactive_environment_plugins_directory =
# 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
# (currently just IPython). These will require Docker to be configured and
# have security considerations, so proceed with caution.
#interactive_environment_plugins_directory =
# Each job is given a unique empty directory as its current working directory.
# This option defines in what parent directory those directories will be
@@ -247,18 +254,20 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# used for the cache
#template_cache_path = database/compiled_templates
# 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 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_cache_data_dir = database/citations/data
#citation_cache_lock_dir = database/citations/lock
# External service types config file, defines what types of external_services configurations
# are available in Galaxy (.sample is used if default does not exist).
# External service types config file, defining what types of external_services
# configurations are available in Galaxy (.sample is used if default does not
# exist).
#external_service_type_config_file = config/external_service_types_conf.xml
# Path to the directory containing the external_service_types defined in the config.
# Path to the directory containing the external_service_types defined in the
# config.
#external_service_type_path = external_service_types
# Tools with a number of outputs not known until runtime can write these
@@ -316,10 +325,11 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# -- Mail and notification
# Galaxy sends mail for various things: Subscribing users to the mailing list
# if they request it, emailing password resets, notification from the Galaxy
# Sample Tracking system, 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 sends mail for various things: subscribing users to the mailing list
# if they request it, password resets, notifications from the Galaxy Sample
# Tracking system, 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 = None
@@ -337,37 +347,44 @@ paste.app_factory = galaxy.web.buildapp:app_factory
#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.
# 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 = None
# Activation email is used as a sender ('from' field) for the account activation mail.
# We recommend using string in the following format: Galaxy Project <galaxy-no-reply@example.com>
# Activation email is used as a sender ('from' field) for the account
# activation mail. We recommend using string in the following format:
# Galaxy Project <galaxy-no-reply@example.com>
#activation_email = None
# URL of the support resource for the galaxy instance. Used in activation emails.
# URL of the support resource for the galaxy instance. Used in activation
# emails.
#instance_resource_url = http://wiki.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 BL they are refused the registration.
# 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.
# 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.
# -- Account activation
# This is user account activation feature global flag. If set to "False" the rest of the Account
# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration).
# Note the activation is also not working in case the smtp server is not defined.
# 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. Activation is not forced (login is not disabled) until
# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content).
# In hours. Default is 3. Enter 0 to disable grace period.
# Users with OpenID logins have grace period forever.
# 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 (see inactivity_box_content). Default is 3. Enter 0 to disable grace
# period.
# Users with OpenID logins have grace period forever.
#activation_grace_period = 0
# Used for warning box for inactive accounts (unable to run jobs).
@@ -378,7 +395,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# -- Analytics
# You can enter tracking code here to track visitor's behavior
# through your Google Analytics account. Example: UA-XXXXXXXX-Y
# through your Google Analytics account. Example: UA-XXXXXXXX-Y
#ga_code = None
# -- Display sites
@@ -401,17 +418,19 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# 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.
# 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.
# 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
# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code.
# -- Next gen LIMS interface on top of existing Galaxy Sample/Request
# management code.
use_nglims = False
nglims_config_file = tool-data/nglims.yaml
@@ -428,18 +447,20 @@ nglims_config_file = tool-data/nglims.yaml
# Format string used when showing date and time information.
# The string may contain:
# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ),
# - the directives used by Python time.strftime() function (see
# http://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).
# - $iso8601 (complete format string as specified by ISO 8601 international
# standard).
# pretty_datetime_format = $locale (UTC)
# URL (with schema http/https) of the Galaxy instance as accessible within your local
# network - if specified used as a default by pulsar file staging and IPython docker
# container for communicating back with Galaxy via the API.
# URL (with schema http/https) of the Galaxy instance as accessible within your
# local network - if specified used as a default by pulsar file staging and
# IPython Docker container for communicating back with Galaxy via the API.
#galaxy_infrastructure_url = http://localhost:8080
# The URL of the page to display in Galaxy's middle pane when loaded. This can be
# an absolute or relative URL.
# The URL of the page to display in Galaxy's middle pane when loaded. This can
# be an absolute or relative URL.
#welcome_url = /static/welcome.html
# The URL linked by the "Galaxy/brand" text.
@@ -470,7 +491,7 @@ nglims_config_file = tool-data/nglims.yaml
# The URL linked by the "Galaxy Q&A" link in the "Help" menu
# The Galaxy Q&A site is under development; when the site is done, this URL
# will be set and uncommented.
#qa_url =
#qa_url =
# Serve static content, which must be enabled if you're not serving it via a
# proxy server. These options should be self explanatory and so are not
@@ -527,9 +548,9 @@ nglims_config_file = tool-data/nglims.yaml
# will cause modern web browsers to not allow Galaxy to be embedded in
# the frames of web applications hosted at other hosts - this can help
# prevent a class of attack called clickjacking
# (https://www.owasp.org/index.php/Clickjacking). If you configure a
# (https://www.owasp.org/index.php/Clickjacking). If you configure a
# proxy in front of Galaxy - please ensure this header remains intact
# to protect your users. Uncomment and leave empty to not set the
# to protect your users. Uncomment and leave empty to not set the
# `X-Frame-Options` header.
#x_frame_options = SAMEORIGIN
@@ -545,10 +566,10 @@ nglims_config_file = tool-data/nglims.yaml
#nginx_upload_path = False
# Have Galaxy manage dynamic proxy component for routing requests to other
# services based on Galaxy's session cookie. It will attempt to do this by
# services based on Galaxy's session cookie. It will attempt to do this by
# default though you do need to install node+npm and do an npm install from
# `lib/galaxy/web/proxy/js`. It is generally more robust to configure this
# externally managing it however Galaxy is managed. If True Galaxy will only
# `lib/galaxy/web/proxy/js`. It is generally more robust to configure this
# externally managing it however Galaxy is managed. If True Galaxy will only
# launch the proxy if it is actually going to be used (e.g. for IPython).
#dynamic_proxy_manage=True
@@ -564,7 +585,8 @@ nglims_config_file = tool-data/nglims.yaml
# Enable verbose debugging of Galaxy-managed dynamic proxy.
#dynamic_proxy_debug=False
# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL)
# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to
# nodejs to wrap connections in SSL).
#dynamic_proxy_external_proxy=False
# -- Logging and Debugging
@@ -582,28 +604,28 @@ nglims_config_file = tool-data/nglims.yaml
# Turn on logging of application events and some user events to the database.
#log_events = True
# Turn on logging of user actions to the database. Actions currently logged are
# grid views, tool searches, and use of "recently" used tools menu. The
# Turn on logging of user actions to the database. Actions currently logged
# are grid views, tool searches, and use of "recently" used tools menu. The
# log_events and log_actions functionality will eventually be merged.
#log_actions = True
# Sanitize All HTML Tool Output By default, all tool output served as
# 'text/html' will be sanitized thoroughly. This can be disabled if
# you have special tools that require unaltered output. WARNING:
# Disabling this does make the Galxy instance susceptible to XSS
# attacks initiated by your users.
# Sanitize all HTML tool output. By default, all tool output served as
# 'text/html' will be sanitized thoroughly. This can be disabled if you have
# special tools that require unaltered output. WARNING: disabling this does
# make the Galaxy instance susceptible to XSS attacks initiated by your users.
#sanitize_all_html = True
# By default Galaxy will serve non-HTML tool output that may potentially
# contain browser executable JavaScript content as plain text. This will for
# contain browser executable JavaScript content as plain text. This will for
# instance cause SVG datasets to not render properly and so may be disabled
# by setting the following option to True.
#serve_xss_vulnerable_mimetypes = False
# Set the following to True to use ipython nbconvert to build HTML from IPython
# notebooks in Galaxy histories. This process may allow users to execute arbitrary
# code or serve arbitrary HTML. If enabled ipython must be available and on Galaxy's
# PATH, to do this run `pip install jinja2 pygments ipython` in Galaxy's virtualenv.
# Set the following to True to use IPython nbconvert to build HTML from IPython
# notebooks in Galaxy histories. This process may allow users to execute
# arbitrary code or serve arbitrary HTML. If enabled, IPython must be
# available and on Galaxy's PATH, to do this run
# `pip install jinja2 pygments ipython` in Galaxy's virtualenv.
#trust_ipython_notebook_conversion = False
# Debug enables access to various config options useful for development and
@@ -659,7 +681,7 @@ use_interactive = True
# if testing shows that Galaxy is able to create files using these formats.
# Specific formats can be disabled with this option, separate more than one
# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'.
#disable_library_comptypes =
#disable_library_comptypes =
# Some sequencer integration features in beta allow you to automatically
# transfer datasets. This is done using a lightweight transfer manager which
@@ -710,10 +732,11 @@ use_interactive = True
#remote_user_header = HTTP_REMOTE_USER
# If use_remote_user is enabled, anyone who can log in to the Galaxy host may
# impersonate any other user by simply sending the appropriate header. Thus a
# impersonate any other user by simply sending the appropriate header. Thus a
# secret shared between the upstream proxy server, and Galaxy is required.
# If anyone other than the Galaxy user is using the server, then apache/nginx should
# pass a value in the header 'GX_SECRET' that is identical the one below
# If anyone other than the Galaxy user is using the server, then apache/nginx
# should pass a value in the header 'GX_SECRET' that is identical to the one
# below.
#remote_user_secret = USING THE DEFAULT IS NOT SECURE!
# If use_remote_user is enabled, you can set this to a URL that will log your
@@ -798,8 +821,9 @@ use_interactive = True
#api_allow_run_as = None
# Master key that allows many API admin actions to be used without actually
# having a defined admin user in the database/config. Only set this if you need
# to bootstrap Galaxy, you probably do not want to set this on public servers.
# having a defined admin user in the database/config. Only set this if you
# need to bootstrap Galaxy, you probably do not want to set this on public
# servers.
#master_api_key = changethis
# Enable tool tags (associating tools with tags). This has its own option
@@ -807,7 +831,7 @@ use_interactive = True
# large servers.
#enable_tool_tags = False
# Enable a feature when running workflows. When enabled, default datasets
# Enable a feature when running workflows. When enabled, default datasets
# are selected for "Set at Runtime" inputs from the history such that the
# same input will not be selected twice, unless there are more inputs than
# compatible datasets in the history.
@@ -843,7 +867,7 @@ use_interactive = True
# File where Data Managers are configured (.sample used if default does not
# exist)
#data_manager_config_file = config/data_manager_conf.xml
# File where Tool Shed based Data Managers are configured
# File where Tool Shed based Data Managers are configured
#shed_data_manager_config_file = config/shed_data_manager_conf.xml
# Directory to store Data Manager based tool-data; defaults to tool_data_path
#galaxy_data_manager_data_path = tool-data
@@ -870,7 +894,8 @@ use_interactive = True
# following option to True or False.
#track_jobs_in_database = None
# This enables splitting of jobs into tasks, if specified by the particular tool config.
# This enables splitting of jobs into tasks, if specified by the particular tool
# config.
# This is a new feature and not recommended for production servers yet.
#use_tasked_jobs = False
#local_task_queue_workers = 2
@@ -921,7 +946,8 @@ use_interactive = True
# Optional file containing job resource data entry fields definition.
# These fields will be presented to users in the tool forms and allow them to
# overwrite default job resources such as number of processors, memory, and walltime.
# overwrite default job resources such as number of processors, memory and
# walltime.
#job_resource_params_file = config/job_resource_params_conf.xml
# If using job concurrency limits (configured in job_config_file), several
@@ -940,7 +966,7 @@ use_interactive = True
# the following lines. tool_* filters will be applied for all users
# and can not be changed by them. user_tool_* filters will be shown
# under user preferences and can be toogled on and off by
# runtime. Example shown below are not real defaults (no custom
# runtime. Example shown below are not real defaults (no custom
# filters applied by defualt) but can be enabled with by renaming the
# example.py.sample in the filters directory to example.py.
@@ -972,11 +998,12 @@ use_interactive = True
# ---- Galaxy External Message Queue -------------------------------------------------
# Galaxy uses AMQ protocol to receive messages from external sources like
# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation.
# For Galaxy to receive messages from a message queue the RabbitMQ server has
# to be set up with a user account and other parameters listed below. The 'host'
# and 'port' fields should point to where the RabbitMQ server is running.
# Galaxy uses Advanced Message Queuing Protocol (AMQP) to receive messages from
# external sources like barcode scanners. Galaxy has been tested against
# RabbitMQ AMQP implementation. For Galaxy to receive messages from a message
# queue, the RabbitMQ server has to be set up with a user account and other
# parameters listed below. The 'host' and 'port' fields should point to where
# the RabbitMQ server is running.
[galaxy_amqp]