3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/156321d8d23b/ Changeset: 156321d8d23b User: nsoranzo Date: 2015-01-29 13:52:19+00:00 Summary: Fix INTEGRATED_TOOL_PANEL_DESCRIPTION . Affected #: 1 file diff -r 2171bcc223ca38613f50bba79df7739aefeb701b -r 156321d8d23bb777be1b5dde6b89c1bb776b9ddd lib/galaxy/tools/toolbox/base.py --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -38,13 +38,17 @@ INTEGRATED_TOOL_PANEL_DESCRIPTION = """ -This is Galaxy's integrated tool panel and probably should not be modified -directly. It will be regenerated each time Galaxy starts up. To modify locally -managed tools (e.g. from tool_conf.xml) modify that file directly and restart -Galaxy. Whenever possible Tool Shed managed tools (e.g. from shed_tool_conf.xml) -should be managed from within the Galaxy interface of via is UI - but if changes -are nessecary (such as to hide a tool or re-assign its section) modify that file -and restart Galaxy. +This is Galaxy's integrated tool panel and should be modified directly only for +reordering tools inside a section. Each time Galaxy starts up, this file is +synchronized with the various tool config files: tools, sections and labels +added to one of these files, will be added also here in the appropriate place, +while elements removed from the tool config files will be correspondingly +deleted from this file. +To modify locally managed tools (e.g. from tool_conf.xml) modify that file +directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g. +from shed_tool_conf.xml) should be managed from within the Galaxy interface or +via its API - but if changes are necessary (such as to hide a tool or re-assign +its section) modify that file and restart Galaxy. """ https://bitbucket.org/galaxy/galaxy-central/commits/d55ccd0bd71e/ Changeset: d55ccd0bd71e User: nsoranzo Date: 2015-01-29 14:43:59+00:00 Summary: Enhancements for galaxy.ini documentation Affected #: 1 file diff -r 156321d8d23bb777be1b5dde6b89c1bb776b9ddd -r d55ccd0bd71e688c69753edf15cbff2f6a2b82ba config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -42,7 +42,8 @@ # Number of threads in the web server thread pool. #threadpool_workers = 10 -# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +# Set the number of seconds a thread can work before you should kill it +# (assuming it will never finish) to 3 hours. Default is 600 (10 minutes). threadpool_kill_thread_limit = 10800 # ---- Filters -------------------------------------------------------------- @@ -172,10 +173,11 @@ # install from in the admin interface (.sample used if default does not exist). #tool_sheds_config_file = config/tool_sheds_conf.xml -# If the following option is set to True - Galaxy will monitor individual tools -# and tool directories specified in tool_conf.xml for changes and reload these -# tools. Watchdog must be installed and available to Galaxy to use this option. -# See https://pypi.python.org/pypi/watchdog. +# 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. #watch_tools = False # Enable automatic polling of relative tool sheds to see if any updates @@ -685,6 +687,8 @@ # used by the algorithm that encodes and decodes these values. It can be any # string. If left unchanged, anyone could construct a cookie that would grant # them access to others' sessions. +# One simple way to generate a value for this is with the shell command: +# python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' ' #id_secret = USING THE DEFAULT IS NOT SECURE! # User authentication can be delegated to an upstream proxy server (usually https://bitbucket.org/galaxy/galaxy-central/commits/8a234cd86e8a/ Changeset: 8a234cd86e8a User: nsoranzo Date: 2015-01-29 14:47:47+00:00 Summary: Whitespace fixes. 80 character limit. Small rewordings. Affected #: 1 file diff -r d55ccd0bd71e688c69753edf15cbff2f6a2b82ba -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -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 @@ #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 @@ # 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 @@ # 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 @@ #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 @@ #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 @@ # 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 @@ # -- 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 @@ #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 @@ # -- 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 @@ # 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 @@ # 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 @@ # 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 @@ # 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 @@ #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 @@ # 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 @@ # 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 @@ # 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 @@ #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 @@ #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 @@ # 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 @@ # 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 @@ # 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 @@ # 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 @@ # 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 @@ # ---- 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] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.