diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 618defd1bf3..398ca602f96 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -222,7 +222,7 @@ functionality is largely untested in modern Galaxy releases and has serious issues such as #7273 and the possibility of slowing down Galaxy startup, so the default and recommended value is - False. + false. :Default: ``false`` :Type: bool @@ -271,14 +271,13 @@ ~~~~~~~~~~~~~~~~~~~~~~~ :Description: - 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 + Various dependency resolver configuration parameters will have + defaults set relative to this path, such as the default conda + prefix, default Galaxy packages path, legacy tool shed + dependencies path, and the dependency cache directory. 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. + with dependencies from the Tool Shed or in Conda will fail. :Default: ``database/dependencies`` :Type: str @@ -360,7 +359,7 @@ ~~~~~~~~~~~~~~~~~~~~~~ :Description: - Set to True to instruct Galaxy to look for and install missing + Set to true to instruct Galaxy to look for and install missing tool dependencies before each job runs. :Default: ``false`` :Type: bool @@ -371,7 +370,7 @@ ~~~~~~~~~~~~~~~~~~~ :Description: - Set to True to instruct Galaxy to install Conda from the web + 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. :Default: ``true`` @@ -383,7 +382,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - You must set this to True if conda_prefix and + 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 @@ -402,10 +401,12 @@ 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 + share. Set this 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. + to your cluster. This only affects tools where some requirements + can be resolved but not others, most modern best practice tools + can use prebuilt environments in the Conda directory. :Default: ``false`` :Type: bool @@ -428,7 +429,7 @@ :Description: 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 + tools for the first time. Set this to false if you prefer dependencies to be cached only when installing new tools. :Default: ``true`` :Type: bool @@ -451,7 +452,7 @@ ~~~~~~~~~~~~~~~ :Description: - Set to True to enable monitoring of tools and tool directories + 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.org/project/watchdog/ ) must be installed @@ -469,7 +470,7 @@ ~~~~~~~~~~~~~~~~~~~ :Description: - Set to True to enable monitoring of dynamic job rules. If changes + Set to true to enable monitoring of dynamic job rules. If changes are found, rules are automatically reloaded. Takes the same values as the 'watch_tools' option. :Default: ``false`` @@ -535,7 +536,7 @@ `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_auto_init is set to false. :Default: ``database/dependencies/involucro`` :Type: str @@ -660,7 +661,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Set to True to enable monitoring of the tool_data and + 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 ( @@ -716,7 +717,7 @@ :Description: Enable sniffing of compressed datatypes. This can be configured/overridden on a per-datatype basis in the - datatypes_conf.xml file. With this option set to False the + datatypes_conf.xml file. With this option set to false the compressed datatypes will be unpacked before sniffing. :Default: ``true`` :Type: bool @@ -767,7 +768,7 @@ :Description: To run interactive environment containers in Docker Swarm mode (on - an existing swarm), set this option to True and set + 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` @@ -1099,9 +1100,9 @@ ~~~~~~~~~~~~~~~~~~~~~~ :Description: - 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 + 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. :Default: ``false`` @@ -1176,9 +1177,9 @@ 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 specified - 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 + files. If use_remote_user is set to 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 @@ -1197,15 +1198,15 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - 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. + Set this to false to disable the old-style display applications + that are hardcoded into datatype classes. 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. :Default: ``true`` :Type: bool @@ -1576,7 +1577,7 @@ For help on configuring the Advanced proxy features, see: https://docs.galaxyproject.org/en/master/admin/production.html Apache can handle file downloads (Galaxy-to-user) via - mod_xsendfile. Set this to True to inform Galaxy that + mod_xsendfile. Set this to true to inform Galaxy that mod_xsendfile is enabled upstream. :Default: ``false`` :Type: bool @@ -1697,9 +1698,9 @@ other 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 launch the proxy if - it is actually going to be used (e.g. for Jupyter). + more robust to configure this externally, managing it in the same + way Galaxy itself is managed. If true, Galaxy will only launch + the proxy if it is actually going to be used (e.g. for Jupyter). :Default: ``true`` :Type: bool @@ -1733,7 +1734,8 @@ :Description: Set the port and IP for the dynamic proxy to bind to, this must - match the external configuration if dynamic_proxy_manage is False. + match the external configuration if dynamic_proxy_manage is set to + false. :Default: ``8800`` :Type: int @@ -1744,7 +1746,8 @@ :Description: Set the port and IP for the dynamic proxy to bind to, this must - match the external configuration if dynamic_proxy_manage is False. + match the external configuration if dynamic_proxy_manage is set to + false. :Default: ``0.0.0.0`` :Type: str @@ -1837,7 +1840,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - If True, Galaxy will attempt to configure a simple root logger if + If true, Galaxy will attempt to configure a simple root logger if a "loggers" section does not appear in this configuration file. :Default: ``true`` :Type: bool @@ -1984,8 +1987,7 @@ By default Galaxy will serve non-HTML tool output that may potentially 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. + properly and so may be disabled by setting this option to true. :Default: ``false`` :Type: bool @@ -2011,12 +2013,11 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - Set the following to True to use Jupyter nbconvert to build HTML - from Jupyter notebooks in Galaxy histories. This process may - allow users to execute arbitrary code or serve arbitrary HTML. If - enabled, Jupyter must be available and on Galaxy's PATH, to do - this run `pip install jinja2 pygments jupyter` in Galaxy's - virtualenv. + Set to true to use Jupyter nbconvert to build HTML from Jupyter + notebooks in Galaxy histories. This process may allow users to + execute arbitrary code or serve arbitrary HTML. If enabled, + Jupyter must be available and on Galaxy's PATH, to do this run + `pip install jinja2 pygments jupyter` in Galaxy's virtualenv. :Default: ``false`` :Type: bool @@ -2294,7 +2295,7 @@ allowing admins to paste filesystem paths to files and directories in a box, and these paths will be added to a library. For history uploads, this allows pasting in paths as URIs. (i.e. prefixed with - file://). Set to True to enable. Please note the security + file://). Set to true to enable. Please note the security implication that this will give Galaxy Admins access to anything your Galaxy user has access to. :Default: ``false`` @@ -2559,8 +2560,8 @@ :Description: If your proxy and/or authentication source does not normalize - e-mail addresses or user names being passed to Galaxy - set the - following option to True to force these to lower case. + e-mail addresses or user names being passed to Galaxy - set this + option to true to force these to lower case. :Default: ``false`` :Type: bool @@ -2609,7 +2610,7 @@ :Description: Show the site's welcome page (see welcome_url) alongside the login - page (even if require_login is True) + page (even if require_login is true). :Default: ``false`` :Type: bool @@ -2641,7 +2642,7 @@ :Description: Allow administrators to log in as other users (useful for - debugging) + debugging). :Default: ``false`` :Type: bool @@ -2674,7 +2675,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ :Description: - By default, users' data will be public, but setting this to True + By default, users' data will be public, but setting this to true will cause it to be private. Does not affect existing users and data, only ones created after this option is set. Users may still change their default back to public. @@ -2687,14 +2688,14 @@ ~~~~~~~~~~~~~~~~~~~~ :Description: - Expose user list. Setting this to True will expose the user list + Expose user list. Setting this to true will expose the user list to authenticated users. This makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and have the correct user show up. This makes less sense on large public Galaxy instances where that data shouldn't be exposed. For semi-public Galaxies, it may make sense to expose just the username and not email, or vice versa. If enable_beta_gdpr is set - to True, then this option will be overridden and set to False. + to true, then this option will be overridden and set to false. :Default: ``false`` :Type: bool @@ -2704,14 +2705,14 @@ ~~~~~~~~~~~~~~~~~~~~~ :Description: - Expose user list. Setting this to True will expose the user list + Expose user list. Setting this to true will expose the user list to authenticated users. This makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and have the correct user show up. This makes less sense on large public Galaxy instances where that data shouldn't be exposed. For semi-public Galaxies, it may make sense to expose just the username and not email, or vice versa. If enable_beta_gdpr is set - to True, then this option will be overridden and set to False. + to true, then this option will be overridden and set to false. :Default: ``false`` :Type: bool @@ -2989,9 +2990,9 @@ 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. When - False, the most recently added compatible item in the history will + false, the most recently added compatible item in the history will be used for each "Set at Runtime" input, independent of others in - the Workflow + the workflow. :Default: ``false`` :Type: bool @@ -3002,7 +3003,7 @@ :Description: The URL to the myExperiment instance being used (omit scheme but - include port) + include port). :Default: ``www.myexperiment.org:80`` :Type: str @@ -3062,8 +3063,8 @@ ~~~~~~~~~~~~~~~~~~~~ :Description: - This should be set to False to prevent Galaxy from deleting - uploaded FTP files as it imports them. + Set to false to prevent Galaxy from deleting uploaded FTP files as + it imports them. :Default: ``true`` :Type: bool @@ -3199,6 +3200,20 @@ :Type: seq +~~~~~~~~~~~~~~~~~~~~~~~~~ +``dependency_resolution`` +~~~~~~~~~~~~~~~~~~~~~~~~~ + +:Description: + Alternative representation of various dependency resolution + parameters. Takes the dictified version of a DependencyManager + object - so this is ideal for automating the configuration of + dependency resolution from one application that uses a + DependencyManager to another. +:Default: ``None`` +:Type: map + + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``default_job_resubmission_condition`` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -3279,7 +3294,7 @@ fail. In these instances, you can choose to retry setting it internally or leave it in a failed state (since retrying internally may cause the Galaxy process to be unresponsive). If - this option is set to False, the user will be given the option to + this option is set to false, the user will be given the option to retry externally, or set metadata manually (when possible). :Default: ``true`` :Type: bool @@ -3499,7 +3514,7 @@ several extra database queries must be performed to determine the number of jobs a user has dispatched to a given destination. By default, these queries will happen for every job that is waiting - to run, but if cache_user_job_count is set to True, it will only + to run, but if cache_user_job_count is set to true, it will only happen once per iteration of the handler queue. Although better for performance due to reduced queries, the trade-off is a greater possibility that jobs will be dispatched past the configured diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 79ba81fb9d6..c0485138c37 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -194,7 +194,7 @@ galaxy: # Galaxy code distribution to the Tool Shed. This functionality is # largely untested in modern Galaxy releases and has serious issues # such as #7273 and the possibility of slowing down Galaxy startup, so - # the default and recommended value is False. + # the default and recommended value is false. #check_migrate_tools: false # Tool config maintained by tool migration scripts. If you use the @@ -215,14 +215,13 @@ galaxy: # an attribute in the 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. + # Various dependency resolver configuration parameters will have + # defaults set relative to this path, such as the default conda + # prefix, default Galaxy packages path, legacy tool shed dependencies + # path, and the dependency cache directory. 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 or in Conda will fail. #tool_dependency_dir: database/dependencies # The dependency resolvers config file specifies an ordering and @@ -254,16 +253,16 @@ galaxy: # Use locally-built conda packages. #conda_use_local: false - # Set to True to instruct Galaxy to look for and install missing tool + # 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 + # 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 + # 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 @@ -274,10 +273,12 @@ galaxy: # 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 + # share. Set this 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. + # your cluster. This only affects tools where some requirements can + # be resolved but not others, most modern best practice tools can use + # prebuilt environments in the Conda directory. #use_cached_dependency_manager: false # By default the tool_dependency_cache_dir is the _cache directory of @@ -286,7 +287,7 @@ galaxy: # 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 + # first time. Set this to false if you prefer dependencies to be # cached only when installing new tools. #precache_dependencies: true @@ -295,7 +296,7 @@ galaxy: # not exist). #tool_sheds_config_file: config/tool_sheds_conf.xml - # Set to True to enable monitoring of tools and tool directories + # 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.org/project/watchdog/ ) must be installed and available @@ -306,7 +307,7 @@ galaxy: # scenarios than the watchdog default. #watch_tools: 'false' - # Set to True to enable monitoring of dynamic job rules. If changes + # Set to true to enable monitoring of dynamic job rules. If changes # are found, rules are automatically reloaded. Takes the same values # as the 'watch_tools' option. #watch_job_rules: 'false' @@ -344,7 +345,7 @@ galaxy: # `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. + # is set to false. #involucro_path: database/dependencies/involucro # Install involucro as needed to build Docker or Singularity @@ -399,7 +400,7 @@ galaxy: # 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 + # 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 ( @@ -427,7 +428,7 @@ galaxy: # Enable sniffing of compressed datatypes. This can be # configured/overridden on a per-datatype basis in the - # datatypes_conf.xml file. With this option set to False the + # datatypes_conf.xml file. With this option set to false the # compressed datatypes will be unpacked before sniffing. #sniff_compressed_dynamic_datatypes_default: true @@ -450,7 +451,7 @@ galaxy: #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 + # 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` @@ -599,7 +600,7 @@ 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 + # 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 @@ -633,10 +634,10 @@ galaxy: # 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 specified 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 + # use_remote_user is set to 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 @@ -646,15 +647,14 @@ galaxy: # 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. + # Set this to false to disable the old-style display applications that + # are hardcoded into datatype classes. 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. @@ -804,7 +804,7 @@ galaxy: # For help on configuring the Advanced proxy features, see: # https://docs.galaxyproject.org/en/master/admin/production.html # Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. - # Set this to True to inform Galaxy that mod_xsendfile is enabled + # Set this to true to inform Galaxy that mod_xsendfile is enabled # upstream. #apache_xsendfile: false @@ -862,9 +862,9 @@ galaxy: # other 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 launch the proxy if it is - # actually going to be used (e.g. for Jupyter). + # robust to configure this externally, managing it in the same way + # Galaxy itself is managed. If true, Galaxy will only launch the + # proxy if it is actually going to be used (e.g. for Jupyter). #dynamic_proxy_manage: true # As of 16.04 Galaxy supports multiple proxy types. The original @@ -877,11 +877,13 @@ galaxy: #dynamic_proxy_session_map: database/session_map.sqlite # Set the port and IP for the dynamic proxy to bind to, this must - # match the external configuration if dynamic_proxy_manage is False. + # match the external configuration if dynamic_proxy_manage is set to + # false. #dynamic_proxy_bind_port: 8800 # Set the port and IP for the dynamic proxy to bind to, this must - # match the external configuration if dynamic_proxy_manage is False. + # match the external configuration if dynamic_proxy_manage is set to + # false. #dynamic_proxy_bind_ip: 0.0.0.0 # Enable verbose debugging of Galaxy-managed dynamic proxy. @@ -918,7 +920,7 @@ galaxy: # if you are managing the proxy manually. #dynamic_proxy_golang_api_key: '' - # If True, Galaxy will attempt to configure a simple root logger if a + # If true, Galaxy will attempt to configure a simple root logger if a # "loggers" section does not appear in this configuration file. #auto_configure_logging: true @@ -980,8 +982,7 @@ galaxy: # By default Galaxy will serve non-HTML tool output that may # potentially 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. + # properly and so may be disabled by setting this option to true. #serve_xss_vulnerable_mimetypes: false # Return a Access-Control-Allow-Origin response header that matches @@ -993,11 +994,11 @@ galaxy: # https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS #allowed_origin_hostnames: '' - # Set the following to True to use Jupyter nbconvert to build HTML - # from Jupyter notebooks in Galaxy histories. This process may allow - # users to execute arbitrary code or serve arbitrary HTML. If - # enabled, Jupyter must be available and on Galaxy's PATH, to do this - # run `pip install jinja2 pygments jupyter` in Galaxy's virtualenv. + # Set to true to use Jupyter nbconvert to build HTML from Jupyter + # notebooks in Galaxy histories. This process may allow users to + # execute arbitrary code or serve arbitrary HTML. If enabled, Jupyter + # must be available and on Galaxy's PATH, to do this run `pip install + # jinja2 pygments jupyter` in Galaxy's virtualenv. #trust_jupyter_notebook_conversion: false # Debug enables access to various config options useful for @@ -1127,7 +1128,7 @@ galaxy: # to paste filesystem paths to files and directories in a box, and # these paths will be added to a library. For history uploads, this # allows pasting in paths as URIs. (i.e. prefixed with file://). Set - # to True to enable. Please note the security implication that this + # to true to enable. Please note the security implication that this # will give Galaxy Admins access to anything your Galaxy user has # access to. #allow_path_paste: false @@ -1250,8 +1251,8 @@ galaxy: #remote_user_logout_href: '' # If your proxy and/or authentication source does not normalize e-mail - # addresses or user names being passed to Galaxy - set the following - # option to True to force these to lower case. + # addresses or user names being passed to Galaxy - set this option to + # true to force these to lower case. #normalize_remote_user_email: false # If an e-mail address is specified here, it will hijack remote user @@ -1272,7 +1273,7 @@ galaxy: #require_login: false # Show the site's welcome page (see welcome_url) alongside the login - # page (even if require_login is True) + # page (even if require_login is true). #show_welcome_with_login: false # Allow unregistered users to create new accounts (otherwise, they @@ -1282,7 +1283,8 @@ galaxy: # Allow administrators to delete accounts. #allow_user_deletion: false - # Allow administrators to log in as other users (useful for debugging) + # Allow administrators to log in as other users (useful for + # debugging). #allow_user_impersonation: false # When using LDAP for authentication, allow administrators to pre- @@ -1294,30 +1296,30 @@ galaxy: # by an administrator in the cleanup scripts run via cron) #allow_user_dataset_purge: true - # By default, users' data will be public, but setting this to True + # By default, users' data will be public, but setting this to true # will cause it to be private. Does not affect existing users and # data, only ones created after this option is set. Users may still # change their default back to public. #new_user_dataset_access_role_default_private: false - # Expose user list. Setting this to True will expose the user list to + # Expose user list. Setting this to true will expose the user list to # authenticated users. This makes sharing datasets in smaller galaxy # instances much easier as they can type a name/email and have the # correct user show up. This makes less sense on large public Galaxy # instances where that data shouldn't be exposed. For semi-public # Galaxies, it may make sense to expose just the username and not - # email, or vice versa. If enable_beta_gdpr is set to True, then this - # option will be overridden and set to False. + # email, or vice versa. If enable_beta_gdpr is set to true, then this + # option will be overridden and set to false. #expose_user_name: false - # Expose user list. Setting this to True will expose the user list to + # Expose user list. Setting this to true will expose the user list to # authenticated users. This makes sharing datasets in smaller galaxy # instances much easier as they can type a name/email and have the # correct user show up. This makes less sense on large public Galaxy # instances where that data shouldn't be exposed. For semi-public # Galaxies, it may make sense to expose just the username and not - # email, or vice versa. If enable_beta_gdpr is set to True, then this - # option will be overridden and set to False. + # email, or vice versa. If enable_beta_gdpr is set to true, then this + # option will be overridden and set to false. #expose_user_email: false # Whitelist for local network addresses for "Upload from URL" dialog. @@ -1446,14 +1448,14 @@ galaxy: # 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. When False, + # are more inputs than compatible datasets in the history. When false, # the most recently added compatible item in the history will be used # for each "Set at Runtime" input, independent of others in the - # Workflow + # workflow. #enable_unique_workflow_defaults: false # The URL to the myExperiment instance being used (omit scheme but - # include port) + # include port). #myexperiment_url: www.myexperiment.org:80 # Enable Galaxy's "Upload via FTP" interface. You'll need to install @@ -1478,8 +1480,8 @@ galaxy: # a particular user. #ftp_upload_dir_template: ${ftp_upload_dir}/${ftp_upload_dir_identifier - # This should be set to False to prevent Galaxy from deleting uploaded - # FTP files as it imports them. + # Set to false to prevent Galaxy from deleting uploaded FTP files as + # it imports them. #ftp_upload_purge: true # Enable enforcement of quotas. Quotas can be set from the Admin @@ -1536,6 +1538,13 @@ galaxy: # dependency_resolvers_config_file is used. #dependency_resolvers: null + # Alternative representation of various dependency resolution + # parameters. Takes the dictified version of a DependencyManager + # object - so this is ideal for automating the configuration of + # dependency resolution from one application that uses a + # DependencyManager to another. + #dependency_resolution: null + # When jobs fail due to job runner problems, Galaxy can be configured # to retry these or reroute the jobs to new destinations. Very fine # control of this is available with resubmit declarations in @@ -1576,7 +1585,7 @@ galaxy: # fail. In these instances, you can choose to retry setting it # internally or leave it in a failed state (since retrying internally # may cause the Galaxy process to be unresponsive). If this option is - # set to False, the user will be given the option to retry externally, + # set to false, the user will be given the option to retry externally, # or set metadata manually (when possible). #retry_metadata_internally: true @@ -1696,7 +1705,7 @@ galaxy: # several extra database queries must be performed to determine the # number of jobs a user has dispatched to a given destination. By # default, these queries will happen for every job that is waiting to - # run, but if cache_user_job_count is set to True, it will only happen + # run, but if cache_user_job_count is set to true, it will only happen # once per iteration of the handler queue. Although better for # performance due to reduced queries, the trade-off is a greater # possibility that jobs will be dispatched past the configured limits diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index 9ef5c2c6d88..cee5956577e 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -185,7 +185,7 @@ mapping: tool_config_files (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool Shed. This functionality is largely untested in modern Galaxy releases and has serious issues such as #7273 and the possibility - of slowing down Galaxy startup, so the default and recommended value is False. + of slowing down Galaxy startup, so the default and recommended value is false. migrated_tools_config: type: str @@ -283,7 +283,7 @@ mapping: default: false required: false desc: | - Set to True to instruct Galaxy to look for and install missing tool + Set to true to instruct Galaxy to look for and install missing tool dependencies before each job runs. conda_auto_init: @@ -291,7 +291,7 @@ mapping: default: true required: false desc: | - Set to True to instruct Galaxy to install Conda from the web automatically + 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_copy_dependencies: @@ -299,7 +299,7 @@ mapping: default: false required: false desc: | - You must set this to True if conda_prefix and job_working_directory are not on the same + 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 @@ -312,7 +312,7 @@ mapping: desc: | 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 + job working directory is on a network share. Set this 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. @@ -336,7 +336,7 @@ mapping: desc: | 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. + Set this to false if you prefer dependencies to be cached only when installing new tools. tool_sheds_config_file: type: str @@ -351,7 +351,7 @@ mapping: default: 'false' required: false desc: | - Set to True to enable monitoring of tools and tool directories + 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.org/project/watchdog/ ) must be installed and @@ -366,7 +366,7 @@ mapping: default: 'false' required: false desc: | - Set to True to enable monitoring of dynamic job rules. If changes are + Set to true to enable monitoring of dynamic job rules. If changes are found, rules are automatically reloaded. Takes the same values as the 'watch_tools' option. @@ -416,7 +416,7 @@ mapping: 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_auto_init is set to false. involucro_auto_init: type: bool @@ -505,7 +505,7 @@ mapping: default: 'false' required: false desc: | - Set to True to enable monitoring of the tool_data and shed_tool_data_path + 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.org/project/watchdog/ ) must be installed and @@ -546,7 +546,7 @@ mapping: desc: | Enable sniffing of compressed datatypes. This can be configured/overridden on a per-datatype basis in the datatypes_conf.xml file. - With this option set to False the compressed datatypes will be unpacked + With this option set to false the compressed datatypes will be unpacked before sniffing. @@ -585,7 +585,7 @@ mapping: required: false desc: | 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 + 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 @@ -823,7 +823,7 @@ mapping: default: false required: false desc: | - User account activation feature global flag. If set to "False", the rest of + 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. @@ -881,7 +881,7 @@ mapping: which browsers should be available. URLs and builds available at these browsers are defined in the specified files. - If use_remote_user = True, display application servers will be denied access + If use_remote_user is set to 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 @@ -899,8 +899,8 @@ mapping: default: true required: false desc: | - To disable the old-style display applications that are hardcoded into - datatype classes, set enable_old_display_applications = False. + Set this to false to disable the old-style display applications that + are hardcoded into datatype classes. 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. @@ -1182,7 +1182,7 @@ mapping: https://docs.galaxyproject.org/en/master/admin/production.html Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set - this to True to inform Galaxy that mod_xsendfile is enabled upstream. + this to true to inform Galaxy that mod_xsendfile is enabled upstream. nginx_x_accel_redirect_base: type: str @@ -1273,7 +1273,7 @@ mapping: 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 + externally, managing it in the same way Galaxy itself is managed. If true, Galaxy will only launch the proxy if it is actually going to be used (e.g. for Jupyter). dynamic_proxy: @@ -1299,7 +1299,7 @@ mapping: required: false desc: | Set the port and IP for the dynamic proxy to bind to, this must match - the external configuration if dynamic_proxy_manage is False. + the external configuration if dynamic_proxy_manage is set to false. dynamic_proxy_bind_ip: type: str @@ -1307,7 +1307,7 @@ mapping: required: false desc: | Set the port and IP for the dynamic proxy to bind to, this must match - the external configuration if dynamic_proxy_manage is False. + the external configuration if dynamic_proxy_manage is set to false. dynamic_proxy_debug: type: bool @@ -1375,7 +1375,7 @@ mapping: default: true required: false desc: | - If True, Galaxy will attempt to configure a simple root logger if a + If true, Galaxy will attempt to configure a simple root logger if a "loggers" section does not appear in this configuration file. log_level: @@ -1389,7 +1389,7 @@ mapping: logging: type: map - allowempty: True + allowempty: true desc: | Controls where and how the server logs messages. If unset, the default is to log all messages to standard output at the level defined by the `log_level` configuration option. Configuration is described in the @@ -1478,7 +1478,7 @@ mapping: By default Galaxy will serve non-HTML tool output that may potentially 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. + by setting this option to true. allowed_origin_hostnames: type: str @@ -1497,7 +1497,7 @@ mapping: default: false required: false desc: | - Set the following to True to use Jupyter nbconvert to build HTML from Jupyter + Set to true to use Jupyter nbconvert to build HTML from Jupyter notebooks in Galaxy histories. This process may allow users to execute arbitrary code or serve arbitrary HTML. If enabled, Jupyter must be available and on Galaxy's PATH, to do this run @@ -1706,7 +1706,7 @@ mapping: adds an option to the admin library upload tool allowing admins to paste filesystem paths to files and directories in a box, and these paths will be added to a library. For history uploads, this allows pasting in paths as URIs. - (i.e. prefixed with file://). Set to True to enable. Please note the security + (i.e. prefixed with file://). Set to true to enable. Please note the security implication that this will give Galaxy Admins access to anything your Galaxy user has access to. @@ -1902,8 +1902,8 @@ mapping: required: false desc: | If your proxy and/or authentication source does not normalize e-mail - addresses or user names being passed to Galaxy - set the following option - to True to force these to lower case. + addresses or user names being passed to Galaxy - set this option + to true to force these to lower case. single_user: type: str @@ -1939,7 +1939,7 @@ mapping: required: false desc: | Show the site's welcome page (see welcome_url) alongside the login page - (even if require_login is True) + (even if require_login is true). allow_user_creation: type: bool @@ -1961,7 +1961,7 @@ mapping: default: false required: false desc: | - Allow administrators to log in as other users (useful for debugging) + Allow administrators to log in as other users (useful for debugging). show_user_prepopulate_form: type: bool @@ -1985,7 +1985,7 @@ mapping: default: false required: false desc: | - By default, users' data will be public, but setting this to True will cause + By default, users' data will be public, but setting this to true will cause it to be private. Does not affect existing users and data, only ones created after this option is set. Users may still change their default back to public. @@ -1995,30 +1995,30 @@ mapping: default: false required: false desc: | - Expose user list. Setting this to True will expose the user list to + Expose user list. Setting this to true will expose the user list to authenticated users. This makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and have the correct user show up. This makes less sense on large public Galaxy instances where that data shouldn't be exposed. For semi-public Galaxies, it may make sense to expose just the username and not email, or vice versa. - If enable_beta_gdpr is set to True, then this option will be - overridden and set to False. + If enable_beta_gdpr is set to true, then this option will be + overridden and set to false. expose_user_email: type: bool default: false required: false desc: | - Expose user list. Setting this to True will expose the user list to + Expose user list. Setting this to true will expose the user list to authenticated users. This makes sharing datasets in smaller galaxy instances much easier as they can type a name/email and have the correct user show up. This makes less sense on large public Galaxy instances where that data shouldn't be exposed. For semi-public Galaxies, it may make sense to expose just the username and not email, or vice versa. - If enable_beta_gdpr is set to True, then this option will be - overridden and set to False. + If enable_beta_gdpr is set to true, then this option will be + overridden and set to false. fetch_url_whitelist: type: str @@ -2228,15 +2228,15 @@ mapping: 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. - When False, the most recently added compatible item in the history will - be used for each "Set at Runtime" input, independent of others in the Workflow + When false, the most recently added compatible item in the history will + be used for each "Set at Runtime" input, independent of others in the workflow. myexperiment_url: type: str default: www.myexperiment.org:80 required: false desc: | - The URL to the myExperiment instance being used (omit scheme but include port) + The URL to the myExperiment instance being used (omit scheme but include port). ftp_upload_dir: type: str @@ -2280,7 +2280,7 @@ mapping: default: true required: false desc: | - This should be set to False to prevent Galaxy from deleting uploaded FTP files + Set to false to prevent Galaxy from deleting uploaded FTP files as it imports them. enable_quotas: @@ -2455,7 +2455,7 @@ mapping: Although it is fairly reliable, setting metadata can occasionally fail. In these instances, you can choose to retry setting it internally or leave it in a failed state (since retrying internally may cause the Galaxy process to be - unresponsive). If this option is set to False, the user will be given the + unresponsive). If this option is set to false, the user will be given the option to retry externally, or set metadata manually (when possible). max_metadata_value_size: @@ -2621,7 +2621,7 @@ mapping: extra database queries must be performed to determine the number of jobs a user has dispatched to a given destination. By default, these queries will happen for every job that is waiting to run, but if cache_user_job_count is - set to True, it will only happen once per iteration of the handler queue. + set to true, it will only happen once per iteration of the handler queue. Although better for performance due to reduced queries, the trade-off is a greater possibility that jobs will be dispatched past the configured limits if running many handlers.