changeset 12:11393eb1c557 draft

planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d1be332a7da0e53b3e6451f0aeda0675f190dd64

--- a/docker/Dockerfile	Wed May 15 06:54:59 2019 -0400
+++ b/docker/Dockerfile	Thu May 16 10:34:26 2019 -0400
@@ -8,7 +8,7 @@
 
 ENV GALAXY_CONFIG_BRAND="Galaxy PIPE-T"
 ENV ENABLE_TTS_INSTALL True
- 
+
 RUN apt-get -y update
 RUN apt-get install -y libxml2-dev libcurl4-openssl-dev curl libcairo2-dev
 
@@ -16,9 +16,13 @@
 #RUN cp /etc/ssl/private/ssl-cert-snakeoil.key /etc/
 #RUN chown root:ssl-cert /etc/ssl-cert-snakeoil.key
 #RUN sed -i -e "s/\/ssl\/private//g" /etc/postgresql/9.3/main/postgresql.conf
+ADD docker/galaxy.yml /etc/galaxy/galaxy.yml
+# ADD docker/dependency_resolvers_conf.yml /etc/galaxy/dependency_resolvers_conf.yml
+ADD docker/dependency_resolvers_conf.yml $GALAXY_ROOT/config/dependency_resolvers_conf.yml
+
 
 #install pipe_t from toolshed
-ADD tools.yml $GALAXY_ROOT/tools.yaml
+ADD docker/tools.yml $GALAXY_ROOT/tools.yaml
 RUN install-tools $GALAXY_ROOT/tools.yaml && \
     /tool_deps/_conda/bin/conda clean --all --yes
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docker/dependency_resolvers_conf.xml	Thu May 16 10:34:26 2019 -0400
@@ -0,0 +1,53 @@
+<dependency_resolvers>
+  <!-- the default configuration, first look for dependencies installed from the toolshed -->
+  <tool_shed_packages />
+  <!-- then look for env.sh files in directories according to the "galaxy packages" schema.
+       These resolvers can take a base_path attribute to specify where to look for
+       package definitions, but by default look in the directory specified by tool_dependency_dir
+       in Galaxy's config/galaxy.ini -->
+  <galaxy_packages />
+  <!-- check whether the correct version has been installed via conda -->
+  <conda />
+  <!-- look for a "default" symlink pointing to a directory containing an
+       env.sh file for the package in the "galaxy packages" schema -->
+  <galaxy_packages versionless="true" />
+  <!-- look for any version of the dependency installed via conda -->
+  <conda versionless="true" />
+
+  <!-- LMOD dependency resolver (For the LMOD environment modules system - https://github.com/TACC/Lmod) -->
+  <!--
+  The LMOD dependency resolver attributes are:
+  * lmodexec - Path to the lmod executable on your system - Default: value of the "LMOD_CMD" environment variable
+  * settargexec - Path to the settarg executable on your system - Default: value of the "LMOD_SETTARG_CMD" environment variable
+  * modulepath - Path to the folder that contains the LMOD module files on your system - Default: value of the "MODULEPATH" environment variable
+  * versionless - Set it to true to resolve a dependency based on its name only (the version number is ignored) - Default: false
+  * mapping_files - Path to a Yaml configuration file that can be used to link tools requirements with existing LMOD modules - Default: config/lmod_modules_mapping.yml
+  Important notes:
+   - All the above attributes are optional
+   - The value of the lmodexec attribute can't just be "module" because module is actually a bash function and not the real LMOD binary (see the result of the "type module" command)
+   - The value of the modulepath attribute can also be a semicolon separated list of path
+   - In versionless mode, only modules marked as Default will be listed by the "avail" command (The -d option is used)
+   - If the config folder of your Galaxy instance contains a file called "lmod_modules_mapping.yml" (based on the lmod_modules_mapping.yml.sample file) it will be taken into consideration automatically
+  -->
+  <!--
+  <lmod />
+  <lmod versionless="true" />
+  -->
+
+  <!-- Example configuration of modules dependency resolver, uses Environment Modules -->
+  <!--
+  <modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd" />
+  <modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd" versionless="true" default_indicator="default" />
+  Attributes are:
+  * modulecmd - path to modulecmd
+  * versionless - default: false - whether to resolve tools using a version number or not
+  * find_by - directory or avail - use the DirectoryModuleChecker or AvailModuleChecker
+  * prefetch - default: true - in the AvailModuleChecker prefetch module info with 'module avail'
+  * default_indicator - default: '(default)' - what indicate to the AvailModuleChecker that a module is the default version
+  -->
+
+  <!-- other resolvers
+  <tool_shed_tap />
+  <homebrew />
+  -->
+</dependency_resolvers>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/docker/galaxy.yml	Thu May 16 10:34:26 2019 -0400
@@ -0,0 +1,1775 @@
+# Galaxy is configured by default to be usable in a single-user development
+# environment.  To tune the application for a multi-user production
+# environment, see the documentation at:
+#
+#  https://docs.galaxyproject.org/en/master/admin/production.html
+#
+# Throughout this sample configuration file, except where stated otherwise,
+# uncommented values override the default if left unset, whereas commented
+# values are set to the default value.  Relative paths are relative to the root
+# Galaxy directory.
+#
+# Examples of many of these options are explained in more detail in the Galaxy
+# Community Hub.
+#
+#   https://galaxyproject.org/admin/config
+#
+# Config hackers are encouraged to check there before asking for help.
+#
+uwsgi:
+
+  # The address and port on which to listen.  By default, only listen to
+  # localhost (galaxy will not be accessible over the network).  Use
+  # ':8080' to listen on all available network interfaces.
+  http: 127.0.0.1:8080
+
+  # By default uWSGI allocates a very small buffer (4096 bytes) for the
+  # headers of each request. If you start receiving "invalid request
+  # block size" in your logs, it could mean you need a bigger buffer. We
+  # recommend at least 16384.
+  buffer-size: 16384
+
+  # Number of web server (worker) processes to fork after the
+  # application has loaded. If this is set to greater than 1, thunder-
+  # lock likely should be enabled below.
+  processes: 1
+
+  # Number of threads for each web server process.
+  threads: 4
+
+  # Number of threads for serving static content and handling internal
+  # routing requests.
+  offload-threads: 2
+
+  # Mapping to serve style content.
+  static-map: /static/style=static/style/blue
+
+  # Mapping to serve the remainder of the static content.
+  static-map: /static=static
+
+  # Mapping to serve the favicon.
+  static-map: /favicon.ico=static/favicon.ico
+
+  # Enable the master process manager. Disabled by default for maximum
+  # compatibility with CTRL+C, but should be enabled for use with
+  # --daemon and/or production deployments.
+  master: false
+
+  # Path to the application's Python virtual environment. If using Conda
+  # for Galaxy's framework dependencies (not tools!), do not set this.
+  virtualenv: .venv
+
+  # Path to the application's Python library.
+  pythonpath: lib
+
+  # The entry point which returns the web application (e.g. Galaxy,
+  # Reports, etc.) that you are loading.
+  module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
+
+  # Mount the web application (e.g. Galaxy, Reports, etc.) at the given
+  # URL prefix. Cannot be used together with 'module:' above.
+  #mount: /galaxy=galaxy.webapps.galaxy.buildapp:uwsgi_app()
+
+  # Make uWSGI rewrite PATH_INFO and SCRIPT_NAME according to mount-
+  # points. Set this to true if a URL prefix is used.
+  manage-script-name: false
+
+  # It is usually a good idea to set this to ``true`` if processes is
+  # greater than 1.
+  thunder-lock: false
+
+  # Cause uWSGI to respect the traditional behavior of dying on SIGTERM
+  # (its default is to brutally reload workers)
+  die-on-term: true
+
+  # Cause uWSGI to gracefully reload workers and mules upon receipt of
+  # SIGINT (its default is to brutally kill workers)
+  hook-master-start: unix_signal:2 gracefully_kill_them_all
+
+  # Cause uWSGI to gracefully reload workers and mules upon receipt of
+  # SIGTERM (its default is to brutally kill workers)
+  hook-master-start: unix_signal:15 gracefully_kill_them_all
+
+  # Feature necessary for proper mule signal handling
+  py-call-osafterfork: true
+
+  # Ensure application threads will run if `threads` is unset.
+  enable-threads: true
+
+galaxy:
+
+  # When running multiple Galaxy instances under separate URL prefixes
+  # on a single hostname, you will want to set this to the same path as
+  # the prefix set in the uWSGI "mount" configuration option above. This
+  # value becomes the "path" attribute set in the cookie so the cookies
+  # from one instance will not clobber those from another.
+  #cookie_path: ''
+
+  # By default, Galaxy uses a SQLite database at
+  # 'database/universe.sqlite'.  You may use a SQLAlchemy connection
+  # string to specify an external database instead.  This string takes
+  # many options which are explained in detail in the config file
+  # documentation.
+  # database_connection: 'postgresql://galaxypg:galaxypg@localhost/galaxydb'
+
+  # If the server logs errors about not having enough database pool
+  # connections, you will want to increase these values, or consider
+  # running more Galaxy processes.
+  #database_engine_option_pool_size: 5
+
+  # If the server logs errors about not having enough database pool
+  # connections, you will want to increase these values, or consider
+  # running more Galaxy processes.
+  #database_engine_option_max_overflow: 10
+
+  # If using MySQL and the server logs the error "MySQL server has gone
+  # away", you will want to set this to some positive value (7200 should
+  # work).
+  #database_engine_option_pool_recycle: -1
+
+  # If large database query results are causing memory or response time
+  # issues in the Galaxy process, leave the result on the server
+  # instead.  This option is only available for PostgreSQL and is highly
+  # recommended.
+  # database_engine_option_server_side_cursors: true
+
+  # Log all database transactions, can be useful for debugging and
+  # performance profiling.  Logging is done via Python's 'logging'
+  # module under the qualname
+  # 'galaxy.model.orm.logging_connection_proxy'
+  #database_query_profiling_proxy: false
+
+  # If auto-creating a postgres database on startup - it can be based on
+  # an existing template database. This will set that. This is probably
+  # only useful for testing but documentation is included here for
+  # completeness.
+  #database_template: ''
+
+  # Slow query logging.  Queries slower than the threshold indicated
+  # below will be logged to debug.  A value of '0' is disabled.  For
+  # example, you would set this to .005 to log all queries taking longer
+  # than 5 milliseconds.
+  #slow_query_log_threshold: 0
+
+  # Enable's a per request sql debugging option. If this is set to true,
+  # append ?sql_debug=1 to web request URLs to enable detailed logging
+  # on the backend of SQL queries generated during that request. This is
+  # useful for debugging slow endpoints during development.
+  #enable_per_request_sql_debugging: false
+
+  # By default, Galaxy will use the same database to track user data and
+  # tool shed install data.  There are many situations in which it is
+  # valuable to separate these - for instance bootstrapping fresh Galaxy
+  # instances with pretested installs.  The following option can be used
+  # to separate the tool shed install database (all other options listed
+  # above but prefixed with install_ are also available).
+  #install_database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
+
+  # Setting the following option to true will cause Galaxy to
+  # automatically migrate the database forward after updates. This is
+  # not recommended for production use.
+  #database_auto_migrate: false
+
+  # Where dataset files are stored. It must accessible at the same path
+  # on any cluster nodes that will run Galaxy jobs, unless using Pulsar.
+  #file_path: database/files
+
+  # Where temporary files are stored. It must accessible at the same
+  # path on any cluster nodes that will run Galaxy jobs, unless using
+  # Pulsar.
+  #new_file_path: database/tmp
+
+  # Tool config files, defines what tools are available in Galaxy. Tools
+  # can be locally developed or installed from Galaxy tool sheds.
+  # (config/tool_conf.xml.sample will be used if left unset and
+  # config/tool_conf.xml does not exist).
+  #tool_config_file: 'config/tool_conf.xml,config/shed_tool_conf.xml'
+
+  # Enable / disable checking if any tools defined in the above non-shed
+  # tool_config_files (i.e., tool_conf.xml) have been migrated from the
+  # Galaxy code distribution to the Tool Shed. This 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.
+  #check_migrate_tools: false
+
+  # Tool config maintained by tool migration scripts.  If you use the
+  # migration scripts to install tools that have been migrated to the
+  # tool shed upon a new release, they will be added to this tool config
+  # file.
+  #migrated_tools_config: config/migrated_tools_conf.xml
+
+  # File that contains the XML section and tool tags from all tool panel
+  # config files integrated into a single file that defines the tool
+  # panel layout.  This file can be changed by the Galaxy administrator
+  # to alter the layout of the tool panel.  If not present, Galaxy will
+  # create it.
+  #integrated_tool_panel_config: integrated_tool_panel.xml
+
+  # Default path to the directory containing the tools defined in
+  # tool_conf.xml. Other tool config files must include the tool_path as
+  # an attribute in the <toolbox> tag.
+  #tool_path: tools
+
+  # Path to the directory in which tool dependencies are placed.  This
+  # is used by the Tool Shed to install dependencies and can also be
+  # used by administrators to manually install or link to dependencies.
+  # For details, see:   https://galaxyproject.org/admin/config/tool-
+  # dependencies Set the string to None to explicitly disable tool
+  # dependency handling. If this option is set to none or an invalid
+  # path, installing tools with dependencies from the Tool Shed will
+  # fail.
+  # tool_dependency_dir: database/dependencies
+
+  # The dependency resolvers config file specifies an ordering and
+  # options for how Galaxy resolves tool dependencies (requirement tags
+  # in Tool XML). The default ordering is to the use the Tool Shed for
+  # tools installed that way, use local Galaxy packages, and then use
+  # Conda if available. See https://github.com/galaxyproject/galaxy/blob
+  # /dev/doc/source/admin/dependency_resolvers.rst for more information
+  # on these options.
+  # dependency_resolvers_config_file: config/dependency_resolvers_conf.xml
+
+  # conda_prefix is the location on the filesystem where Conda packages
+  # and environments are installed IMPORTANT: Due to a current
+  # limitation in conda, the total length of the conda_prefix and the
+  # job_working_directory path should be less than 50 characters!
+  # conda_prefix: database/dependencies/_conda
+
+  # Override the Conda executable to use, it will default to the one on
+  # the PATH (if available) and then to <conda_prefix>/bin/conda
+  #conda_exec: null
+
+  # Pass debug flag to conda commands.
+  #conda_debug: false
+
+  # conda channels to enable by default (https://conda.io/docs/user-
+  # guide/tasks/manage-channels.html)
+  conda_ensure_channels: 'r,iuc,conda-forge,bioconda,defaults'
+
+  # Set to True to instruct Galaxy to look for and install missing tool
+  # dependencies before each job runs.
+  # conda_auto_install: true
+
+  # Set to True to instruct Galaxy to install Conda from the web
+  # automatically if it cannot find a local copy and conda_exec is not
+  # configured.
+  # conda_auto_init: true
+
+  # You must set this to True if conda_prefix and job_working_directory
+  # are not on the same volume, or some conda dependencies will fail to
+  # execute at job runtime. Conda will copy packages content instead of
+  # creating hardlinks or symlinks. This will prevent problems with some
+  # specific packages (perl, R), at the cost of extra disk space usage
+  # and extra time spent copying packages.
+  #conda_copy_dependencies: true
+
+  # Certain dependency resolvers (namely Conda) take a considerable
+  # amount of time to build an isolated job environment in the
+  # job_working_directory if the job working directory is on a network
+  # share.  Set the following option to True to cache the dependencies
+  # in a folder. This option is beta and should only be used if you
+  # experience long waiting times before a job is actually submitted to
+  # your cluster.
+  # use_cached_dependency_manager: True
+
+  # By default the tool_dependency_cache_dir is the _cache directory of
+  # the tool dependency directory
+  # tool_dependency_cache_dir: database/dependencies/_cache
+
+  # By default, when using a cached dependency manager, the dependencies
+  # are cached when installing new tools and when using tools for the
+  # first time. Set this to False if you prefer dependencies to be
+  # cached only when installing new tools.
+  # precache_dependencies: true
+
+  # File containing the Galaxy Tool Sheds that should be made available
+  # to install from in the admin interface (.sample used if default does
+  # not exist).
+  #tool_sheds_config_file: config/tool_sheds_conf.xml
+
+  # Set to True to enable monitoring of tools and tool directories
+  # listed in any tool config file specified in tool_config_file option.
+  # If changes are found, tools are automatically reloaded.  Watchdog (
+  # https://pypi.org/project/watchdog/ ) must be installed and available
+  # to Galaxy to use this option. Other options include 'auto' which
+  # will attempt to watch tools if the watchdog library is available but
+  # won't fail to load Galaxy if it is not and 'polling' which will use
+  # a less efficient monitoring scheme that may work in wider range of
+  # scenarios than the watchdog default.
+  #watch_tools: 'false'
+
+  # 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'
+
+  # As of 18.09, Galaxy defaults to setting up the object store
+  # configuration for output datasets during the job queue step in job
+  # handlers. This should generally provide for more robust job
+  # submission, more configurability, and a better user experience but
+  # may in some cases slightly slow down the job handler job setup
+  # process. On the off chance that an admin would like to or need to
+  # optimize job handlers at the expense of user experience and web
+  # handling this option will remain for some time by setting this
+  # option to true. This behavior however should be considered
+  # deprecated and this option will likely be removed in future versions
+  # of Galaxy. For more information see
+  # https://github.com/galaxyproject/galaxy/issues/6513.
+  #legacy_eager_objectstore_initialization: false
+
+  # Enable Galaxy to fetch Docker containers registered with quay.io
+  # generated from tool requirements resolved through conda. These
+  # containers (when available) have been generated using mulled -
+  # https://github.com/mulled . These containers are highly beta and
+  # availability will vary by tool. This option will additionally only
+  # be used for job destinations with Docker enabled.
+  #enable_beta_mulled_containers: false
+
+  # Container resolvers configuration (beta). Setup a file describing
+  # container resolvers to use when discovering containers for Galaxy.
+  # If this is set to None, the default containers loaded is determined
+  # by enable_beta_mulled_containers.
+  #containers_resolvers_config_file: ''
+
+  # involucro is a tool used to build Docker containers for tools from
+  # Conda dependencies referenced in tools as `requirement`s. The
+  # following path is the location of involucro on the Galaxy host. This
+  # is ignored if the relevant container resolver isn't enabled, and
+  # will install on demand unless involucro_auto_init is set to False.
+  #involucro_path: database/dependencies/involucro
+
+  # Install involucro as needed to build Docker containers for tools.
+  # Ignored if relevant container resolver is not used.
+  #involucro_auto_init: true
+
+  # Enable automatic polling of relative tool sheds to see if any
+  # updates are available for installed repositories.  Ideally only one
+  # Galaxy server process should be able to check for repository
+  # updates.  The setting for hours_between_check should be an integer
+  # between 1 and 24.
+  #enable_tool_shed_check: false
+
+  # Enable automatic polling of relative tool sheds to see if any
+  # updates are available for installed repositories.  Ideally only one
+  # Galaxy server process should be able to check for repository
+  # updates.  The setting for hours_between_check should be an integer
+  # between 1 and 24.
+  #hours_between_check: 12
+
+  # Enable use of an in-memory registry with bi-directional
+  # relationships between repositories (i.e., in addition to lists of
+  # dependencies for a repository, keep an in-memory registry of
+  # dependent items for each repository.
+  #manage_dependency_relationships: false
+
+  # XML config file that contains data table entries for the
+  # ToolDataTableManager.  This file is manually # maintained by the
+  # Galaxy administrator (.sample used if default does not exist).
+  #tool_data_table_config_path: config/tool_data_table_conf.xml
+
+  # XML config file that contains additional data table entries for the
+  # ToolDataTableManager.  This file is automatically generated based on
+  # the current installed tool shed repositories that contain valid
+  # tool_data_table_conf.xml.sample files.  At the time of installation,
+  # these entries are automatically added to the following file, which
+  # is parsed and applied to the ToolDataTableManager at server start
+  # up.
+  #shed_tool_data_table_config: config/shed_tool_data_table_conf.xml
+
+  # Directory where data used by tools is located.  See the samples in
+  # that directory and the Galaxy Community Hub for help:
+  # https://galaxyproject.org/admin/data-integration
+  #tool_data_path: tool-data
+
+  # Directory where Tool Data Table related files will be placed when
+  # installed from a ToolShed. Defaults to tool_data_path.
+  #shed_tool_data_path: tool-data
+
+  # Set to True to enable monitoring of the tool_data and
+  # shed_tool_data_path directories. If changes in tool data table files
+  # are found, the tool data tables for that data manager are
+  # automatically reloaded. Watchdog (
+  # https://pypi.org/project/watchdog/ ) must be installed and available
+  # to Galaxy to use this option. Other options include 'auto' which
+  # will attempt to use the watchdog library if it is available but
+  # won't fail to load Galaxy if it is not and 'polling' which will use
+  # a less efficient monitoring scheme that may work in wider range of
+  # scenarios than the watchdog default.
+  #watch_tool_data_dir: 'false'
+
+  # File containing old-style genome builds
+  #builds_file_path: tool-data/shared/ucsc/builds.txt
+
+  # Directory where chrom len files are kept, currently mainly used by
+  # trackster
+  #len_file_path: tool-data/shared/ucsc/chrom
+
+  # Datatypes config file(s), defines what data (file) types are
+  # available in Galaxy (.sample is used if default does not exist).  If
+  # a datatype appears in multiple files, the last definition is used
+  # (though the first sniffer is used so limit sniffer definitions to
+  # one file).
+  #datatypes_config_file: config/datatypes_conf.xml
+
+  # 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 before sniffing.
+  #sniff_compressed_dynamic_datatypes_default: true
+
+  # Disable the 'Auto-detect' option for file uploads
+  #datatypes_disable_auto: false
+
+  # Visualizations config directory: where to look for individual
+  # visualization plugins.  The path is relative to the Galaxy root dir.
+  # To use an absolute path begin the path with '/'.  This is a comma
+  # separated list. Defaults to "config/plugins/visualizations".
+  #visualization_plugins_directory: config/plugins/visualizations
+
+  # Interactive environment plugins root directory: where to look for
+  # interactive environment plugins.  By default none will be loaded.
+  # Set to config/plugins/interactive_environments to load Galaxy's
+  # stock plugins. These will require Docker to be configured and have
+  # security considerations, so proceed with caution. The path is
+  # relative to the Galaxy root dir.  To use an absolute path begin the
+  # path with '/'.  This is a comma separated list.
+  #interactive_environment_plugins_directory: null
+
+  # To run interactive environment containers in Docker Swarm mode (on
+  # an existing swarm), set this option to True and set
+  # `docker_connect_port` in the IE plugin config (ini) file(s) of any
+  # IE plugins you have enabled and ensure that you are not using any
+  # `docker run`-specific options in your plugins' `command_inject`
+  # options (swarm mode services run using `docker service create`,
+  # which has a different and more limited set of options). This option
+  # can be overridden on a per-plugin basis by using the `swarm_mode`
+  # option in the plugin's ini config file.
+  #interactive_environment_swarm_mode: false
+
+  # Galaxy can run a "swarm manager" service that will monitor
+  # utilization of the swarm and provision/deprovision worker nodes as
+  # necessary. The service has its own configuration file.
+  #swarm_manager_config_file: config/swarm_manager_conf.yml
+
+  # Interactive tour directory: where to store interactive tour
+  # definition files. Galaxy ships with several basic interface tours
+  # enabled, though a different directory with custom tours can be
+  # specified here. The path is relative to the Galaxy root dir.  To use
+  # an absolute path begin the path with '/'.  This is a comma separated
+  # list.
+  #tour_config_dir: config/plugins/tours
+
+  # Webhooks directory: where to store webhooks - plugins to extend the
+  # Galaxy UI. By default none will be loaded.  Set to
+  # config/plugins/webhooks/demo to load Galaxy's demo webhooks.  To use
+  # an absolute path begin the path with '/'.  This is a comma separated
+  # list. Add test/functional/webhooks to this list to include the demo
+  # webhooks used to test the webhook framework.
+  #webhooks_dir: config/plugins/webhooks
+
+  # Each job is given a unique empty directory as its current working
+  # directory. This option defines in what parent directory those
+  # directories will be created.
+  #job_working_directory: database/jobs_directory
+
+  # If using a cluster, Galaxy will write job scripts and stdout/stderr
+  # to this directory.
+  #cluster_files_directory: database/pbs
+
+  # Mako templates are compiled as needed and cached for reuse, this
+  # directory is used for the cache
+  #template_cache_path: database/compiled_templates
+
+  # Set to false to disable various checks Galaxy will do to ensure it
+  # can run job scripts before attempting to execute or submit them.
+  #check_job_script_integrity: true
+
+  # Number of checks to execute if check_job_script_integrity is
+  # enabled.
+  #check_job_script_integrity_count: 35
+
+  # Time to sleep between checks if check_job_script_integrity is
+  # enabled (in seconds).
+  #check_job_script_integrity_sleep: 0.25
+
+  # Set the default shell used by non-containerized jobs Galaxy-wide.
+  # This defaults to bash for all jobs and can be overridden at the
+  # destination level for heterogeneous clusters. conda job resolution
+  # requires bash or zsh so if this is switched to /bin/sh for instance
+  # - conda resolution should be disabled. Containerized jobs always use
+  # /bin/sh - so more maximum portability tool authors should assume
+  # generated commands run in sh.
+  #default_job_shell: /bin/bash
+
+  # Citation related caching.  Tool citations information maybe fetched
+  # from external sources such as https://doi.org/ by Galaxy - the
+  # following parameters can be used to control the caching used to
+  # store this information.
+  #citation_cache_type: file
+
+  # Citation related caching.  Tool citations information maybe fetched
+  # from external sources such as https://doi.org/ by Galaxy - the
+  # following parameters can be used to control the caching used to
+  # store this information.
+  #citation_cache_data_dir: database/citations/data
+
+  # Citation related caching.  Tool citations information maybe fetched
+  # from external sources such as https://doi.org/ by Galaxy - the
+  # following parameters can be used to control the caching used to
+  # store this information.
+  #citation_cache_lock_dir: database/citations/lock
+
+  # Tools with a number of outputs not known until runtime can write
+  # these outputs to a directory for collection by Galaxy when the job
+  # is done. Previously, this directory was new_file_path, but using one
+  # global directory can cause performance problems, so using
+  # job_working_directory ('.' or cwd when a job is run) is encouraged.
+  # By default, both are checked to avoid breaking existing tools.
+  #collect_outputs_from: 'new_file_path,job_working_directory'
+
+  # Configuration file for the object store If this is set and exists,
+  # it overrides any other objectstore settings.
+  #object_store_config_file: config/object_store_conf.xml
+
+  # Galaxy sends mail for various things: subscribing users to the
+  # mailing list if they request it, password resets, reporting dataset
+  # errors, and sending activation emails. To do this, it needs to send
+  # mail through an SMTP server, which you may define here (host:port).
+  # Galaxy will automatically try STARTTLS but will continue upon
+  # failure.
+  #smtp_server: ''
+
+  # If your SMTP server requires a username and password, you can
+  # provide them here (password in cleartext here, but if your server
+  # supports STARTTLS it will be sent over the network encrypted).
+  #smtp_username: ''
+
+  # If your SMTP server requires a username and password, you can
+  # provide them here (password in cleartext here, but if your server
+  # supports STARTTLS it will be sent over the network encrypted).
+  #smtp_password: ''
+
+  # If your SMTP server requires SSL from the beginning of the
+  # connection
+  #smtp_ssl: false
+
+  # On the user registration form, users may choose to join a mailing
+  # list. This is the address used to subscribe to the list. Uncomment
+  # and leave empty if you want to remove this option from the user
+  # registration form.
+  #mailing_join_addr: [e-mail]
+
+  # Datasets in an error state include a link to report the error.
+  # Those reports will be sent to this address.  Error reports are
+  # disabled if no address is set.  Also this email is shown as a
+  # contact to user in case of Galaxy misconfiguration and other events
+  # user may encounter.
+  #error_email_to: ''
+
+  # Email address to use in the 'From' field when sending emails for
+  # account activations, workflow step notifications and password
+  # resets. We recommend using string in the following format: Galaxy
+  # Project <[e-mail]> If not configured, '<galaxy-
+  # no-reply@HOSTNAME>' will be used.
+  #email_from: ''
+
+  # URL of the support resource for the galaxy instance.  Used in
+  # activation emails.
+  #instance_resource_url: 'https://galaxyproject.org/'
+
+  # E-mail domains blacklist is used for filtering out users that are
+  # using disposable email address during the registration.  If their
+  # address domain matches any domain in the blacklist, they are refused
+  # the registration.
+  #blacklist_file: config/disposable_email_blacklist.conf
+
+  # Registration warning message is used to discourage people from
+  # registering multiple accounts.  Applies mostly for the main Galaxy
+  # instance. If no message specified the warning box will not be shown.
+  #registration_warning_message: Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion.
+
+  # User account activation feature global flag.  If set to "False", the
+  # rest of the Account activation configuration is ignored and user
+  # activation is disabled (i.e. accounts are active since
+  # registration). The activation is also not working in case the SMTP
+  # server is not defined.
+  #user_activation_on: false
+
+  # Activation grace period (in hours).  Activation is not forced (login
+  # is not disabled) until grace period has passed.  Users under grace
+  # period can't run jobs. Enter 0 to disable grace period. Users with
+  # OpenID logins have grace period forever.
+  #activation_grace_period: 3
+
+  # Shown in warning box to users that were not activated yet. In use
+  # only if activation_grace_period is set.
+  #inactivity_box_content: 'Your account has not been activated yet.  Feel free to browse around and see what''s available, but you won''t be able to upload data or run jobs until you have verified your email address.'
+
+  # Password expiration period (in days). Users are required to change
+  # their password every x days. Users will be redirected to the change
+  # password screen when they log in after their password expires. Enter
+  # 0 to disable password expiration.
+  #password_expiration_period: 0
+
+  # Galaxy Session Timeout This provides a timeout (in minutes) after
+  # which a user will have to log back in. A duration of 0 disables this
+  # feature.
+  #session_duration: 0
+
+  # You can enter tracking code here to track visitor's behavior through
+  # your Google Analytics account.  Example: UA-XXXXXXXX-Y
+  #ga_code: ''
+
+  # Galaxy can display data at various external browsers.  These options
+  # specify which browsers should be available.  URLs and builds
+  # available at these browsers are defined in the specifield files.  If
+  # use_remote_user = True, display application servers will be denied
+  # access to Galaxy and so displaying datasets in these sites will
+  # fail. display_servers contains a list of hostnames which should be
+  # allowed to bypass security to display datasets.  Please be aware
+  # that there are security implications if this is allowed.  More
+  # details (including required changes to the proxy server config) are
+  # available in the Apache proxy documentation on the Galaxy Community
+  # Hub.  The list of servers in this sample config are for the UCSC
+  # Main, Test and Archaea browsers, but the default if left commented
+  # is to not allow any display sites to bypass security (you must
+  # uncomment the line below to allow them).
+  #display_servers: 'hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu'
+
+  # To disable the old-style display applications that are hardcoded
+  # into datatype classes, set enable_old_display_applications = False.
+  # This may be desirable due to using the new-style, XML-defined,
+  # display applications that have been defined for many of the
+  # datatypes that have the old-style. There is also a potential
+  # security concern with the old-style applications, where a malicious
+  # party could provide a link that appears to reference the Galaxy
+  # server, but contains a redirect to a third-party server, tricking a
+  # Galaxy user to access said site.
+  #enable_old_display_applications: true
+
+  # Show a message box under the masthead.
+  #message_box_visible: false
+
+  # Show a message box under the masthead.
+  #message_box_content: ''
+
+  # Show a message box under the masthead.
+  #message_box_class: info
+
+  # Append "/{brand}" to the "Galaxy" text in the masthead.
+  #brand: ''
+
+  # Format string used when showing date and time information. The
+  # string may contain: - the directives used by Python time.strftime()
+  # function (see
+  # https://docs.python.org/library/time.html#time.strftime ), - $locale
+  # (complete format string for the server locale), - $iso8601 (complete
+  # format string as specified by ISO 8601 international   standard).
+  #pretty_datetime_format: $locale (UTC)
+
+  # Default localization for Galaxy UI. Allowed values are listed at the
+  # end of client/galaxy/scripts/nls/locale.js. With the default value
+  # (auto), the locale will be automatically adjusted to the user's
+  # navigator language. Users can override this settings in their user
+  # preferences if the localization settings are enabled in
+  # user_preferences_extra_conf.yml
+  #default_locale: auto
+
+  # URL (with schema http/https) of the Galaxy instance as accessible
+  # within your local network - if specified used as a default by pulsar
+  # file staging and Jupyter Docker container for communicating back
+  # with Galaxy via the API.  If you are attempting to setup GIEs on Mac
+  # OS X with Docker for Mac - this should likely be the IP address of
+  # your machine on the virtualbox network (vboxnet0) setup for the
+  # Docker host VM. This can found by running ifconfig and using the IP
+  # address of the network vboxnet0.
+  #galaxy_infrastructure_url: 'http://localhost:8080'
+
+  # If the above URL cannot be determined ahead of time in dynamic
+  # environments but the port which should be used to access Galaxy can
+  # be - this should be set to prevent Galaxy from having to guess.  For
+  # example if Galaxy is sitting behind a proxy with REMOTE_USER enabled
+  # - infrastructure shouldn't talk to Python processes directly and
+  # this should be set to 80 or 443, etc... If unset this file will be
+  # read for a server block defining a port corresponding to the webapp.
+  #galaxy_infrastructure_web_port: 8080
+
+  # 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.
+  #logo_url: /
+
+  # The URL linked by the "Galaxy Help" link in the "Help" menu.
+  #helpsite_url: ''
+
+  # The URL linked by the "Wiki" link in the "Help" menu.
+  #wiki_url: 'https://galaxyproject.org/'
+
+  # The URL linked by the "Support" link in the "Help" menu.
+  #support_url: 'https://galaxyproject.org/support/'
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_url: ''
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_key_name: ''
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_key: ''
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_enable_bug_reports: true
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_never_authenticate: false
+
+  # The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
+  #citation_url: 'https://galaxyproject.org/citing-galaxy'
+
+  # The URL linked by the "Search" link in the "Help" menu.
+  #search_url: 'https://galaxyproject.org/search/'
+
+  # The URL linked by the "Mailing Lists" link in the "Help" menu.
+  #mailing_lists_url: 'https://galaxyproject.org/mailing-lists'
+
+  # The URL linked by the "Videos" link in the "Help" menu.
+  #screencasts_url: 'https://vimeo.com/galaxyproject'
+
+  # Points to the GenomeSpace UI service which will be used by the
+  # GenomeSpace importer and exporter tools
+  #genomespace_ui_url: 'https://gsui.genomespace.org/jsui/'
+
+  # The URL linked by the "Terms and Conditions" link in the "Help"
+  # menu, as well as on the user registration and login forms and in the
+  # activation emails.
+  #terms_url: ''
+
+  # 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: null
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_enabled: true
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_cache_time: 360
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_dir: static/
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_images_dir: static/images
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_favicon_dir: static/favicon.ico
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_scripts_dir: static/scripts/
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_style_dir: static/june_2007_style/blue
+
+  # 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 documented individually.  You can use these paths (or ones
+  # in the proxy server) to point to your own styles.
+  #static_robots_txt: static/robots.txt
+
+  # Incremental Display Options
+  #display_chunk_size: 65536
+
+  # 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
+  # upstream.
+  #apache_xsendfile: false
+
+  # The same download handling can be done by nginx using X-Accel-
+  # Redirect.  This should be set to the path defined in the nginx
+  # config as an internal redirect with access to Galaxy's data files
+  # (see documentation linked above).
+  #nginx_x_accel_redirect_base: ''
+
+  # If using compression in the upstream proxy server, use this option
+  # to disable gzipping of library .tar.gz and .zip archives, since the
+  # proxy server will do it faster on the fly.
+  #upstream_gzip: false
+
+  # The following default adds a header to web request responses that
+  # 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
+  # proxy in front of Galaxy - please ensure this header remains intact
+  # to protect your users.  Uncomment and leave empty to not set the `X
+  # -Frame-Options` header.
+  #x_frame_options: SAMEORIGIN
+
+  # nginx can also handle file uploads (user-to-Galaxy) via
+  # nginx_upload_module. Configuration for this is complex and explained
+  # in detail in the documentation linked above.  The upload store is a
+  # temporary directory in which files uploaded by the upload module
+  # will be placed.
+  #nginx_upload_store: ''
+
+  # This value overrides the action set on the file upload form, e.g.
+  # the web path where the nginx_upload_module has been configured to
+  # intercept upload requests.
+  #nginx_upload_path: ''
+
+  # Galaxy can also use nginx_upload_module to receive files staged out
+  # upon job completion by remote job runners (i.e. Pulsar) that
+  # initiate staging operations on the remote end.  See the Galaxy nginx
+  # documentation for the corresponding nginx configuration.
+  #nginx_upload_job_files_store: ''
+
+  # Galaxy can also use nginx_upload_module to receive files staged out
+  # upon job completion by remote job runners (i.e. Pulsar) that
+  # initiate staging operations on the remote end.  See the Galaxy nginx
+  # documentation for the corresponding nginx configuration.
+  #nginx_upload_job_files_path: ''
+
+  # Galaxy can upload user files in chunks without using nginx. Enable
+  # the chunk uploader by specifying a chunk size larger than 0. The
+  # chunk size is specified in bytes (default: 100MB).
+  #chunk_upload_size: 104857600
+
+  # 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 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).
+  #dynamic_proxy_manage: true
+
+  # As of 16.04 Galaxy supports multiple proxy types. The original
+  # NodeJS implementation, alongside a new Golang single-binary-no-
+  # dependencies version. Valid values are (node, golang)
+  #dynamic_proxy: node
+
+  # The NodeJS dynamic proxy can use an SQLite database or a JSON file
+  # for IPC, set that here.
+  #dynamic_proxy_session_map: database/session_map.sqlite
+
+  # Set the port and IP for the the dynamic proxy to bind to, this must
+  # match the external configuration if dynamic_proxy_manage is False.
+  #dynamic_proxy_bind_port: 8800
+
+  # Set the port and IP for the the dynamic proxy to bind to, this must
+  # match the external configuration if dynamic_proxy_manage is False.
+  #dynamic_proxy_bind_ip: 0.0.0.0
+
+  # 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).
+  #dynamic_proxy_external_proxy: false
+
+  # Additionally, when the dynamic proxy is proxied by an upstream
+  # server, you'll want to specify a prefixed URL so both Galaxy and the
+  # proxy reside under the same path that your cookies are under. This
+  # will result in a url like https://FQDN/galaxy-prefix/gie_proxy for
+  # proxying
+  #dynamic_proxy_prefix: gie_proxy
+
+  # This attribute governs the minimum length of time between
+  # consecutive HTTP/WS requests through the proxy, before the proxy
+  # considers a container as being inactive and kills it.
+  #dynamic_proxy_golang_noaccess: 60
+
+  # In order to kill containers, the golang proxy has to check at some
+  # interval for possibly dead containers. This is exposed as a
+  # configurable parameter, but the default value is probably fine.
+  #dynamic_proxy_golang_clean_interval: 10
+
+  # The golang proxy needs to know how to talk to your docker daemon.
+  # Currently TLS is not supported, that will come in an update.
+  #dynamic_proxy_golang_docker_address: 'unix:///var/run/docker.sock'
+
+  # The golang proxy uses a RESTful HTTP API for communication with
+  # Galaxy instead of a JSON or SQLite file for IPC. If you do not
+  # specify this, it will be set randomly for you. You should set this
+  # 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
+  # "loggers" section does not appear in this configuration file.
+  #auto_configure_logging: true
+
+  # Verbosity of console log messages.  Acceptable values can be found
+  # here: https://docs.python.org/library/logging.html#logging-levels A
+  # custom debug level of "TRACE" is available for even more verbosity.
+  #log_level: DEBUG
+
+  # 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 documentation at:
+  # https://docs.galaxyproject.org/en/master/admin/config_logging.html
+  #logging: null
+
+  # Print database operations to the server log (warning, quite
+  # verbose!).
+  #database_engine_option_echo: false
+
+  # Print database pool operations to the server log (warning, quite
+  # verbose!).
+  #database_engine_option_echo_pool: false
+
+  # 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 log_events and log_actions functionality will
+  # eventually be merged.
+  #log_actions: true
+
+  # Fluentd configuration.  Various events can be logged to the fluentd
+  # instance configured below by enabling fluent_log.
+  #fluent_log: false
+
+  # Fluentd configuration.  Various events can be logged to the fluentd
+  # instance configured below by enabling fluent_log.
+  #fluent_host: localhost
+
+  # Fluentd configuration.  Various events can be logged to the fluentd
+  # instance configured below by enabling fluent_log.
+  #fluent_port: 24224
+
+  # 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
+
+  # Whitelist sanitization file. Datasets created by tools listed in
+  # this file are trusted and will not have their HTML sanitized on
+  # display.  This can be manually edited or manipulated through the
+  # Admin control panel -- see "Manage Display Whitelist"
+  #sanitize_whitelist_file: config/sanitize_whitelist.txt
+
+  # 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.
+  #serve_xss_vulnerable_mimetypes: false
+
+  # Return a Access-Control-Allow-Origin response header that matches
+  # the Origin header of the request if that Origin hostname matches one
+  # of the strings or regular expressions listed here. This is a comma
+  # separated list of hostname strings or regular expressions beginning
+  # and ending with /. E.g.
+  # mysite.com,google.com,usegalaxy.org,/^[\w\.]*example\.com/ See:
+  # 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.
+  #trust_jupyter_notebook_conversion: false
+
+  # Debug enables access to various config options useful for
+  # development and debugging: use_lint, use_profile, use_printdebug and
+  # use_interactive.  It also causes the files used by PBS/SGE
+  # (submission script, output, and error) to remain on disk after the
+  # job is complete.
+  #debug: false
+
+  # Check for WSGI compliance.
+  #use_lint: false
+
+  # Run the Python profiler on each request.
+  #use_profile: false
+
+  # Intercept print statements and show them on the returned page.
+  #use_printdebug: true
+
+  # Enable live debugging in your browser.  This should NEVER be enabled
+  # on a public site.  Enabled in the sample config for development.
+  #use_interactive: true
+
+  # When stopping Galaxy cleanly, how much time to give various
+  # monitoring/polling threads to finish before giving up on joining
+  # them. Set to 0 to disable this and restore the pre-18.01 default
+  # behavior.
+  #monitor_thread_join_timeout: 5
+
+  # Write thread status periodically to 'heartbeat.log',  (careful, uses
+  # disk space rapidly!).  Useful to determine why your processes may be
+  # consuming a lot of CPU.
+  #use_heartbeat: false
+
+  # Control the period (in seconds) between dumps. Use -1 to disable.
+  # Regardless of this setting, if use_heartbeat is enabled, you can
+  # send a Galaxy process (unless running with uWSGI) SIGUSR1 (`kill
+  # -USR1`) to force a dump.
+  #heartbeat_interval: 20
+
+  # Heartbeat log filename. Can accept the template variables
+  # {server_name} and {pid}
+  #heartbeat_log: 'heartbeat_{server_name}.log'
+
+  # Log to Sentry Sentry is an open source logging and error aggregation
+  # platform.  Setting sentry_dsn will enable the Sentry middleware and
+  # errors will be sent to the indicated sentry instance.  This
+  # connection string is available in your sentry instance under
+  # <project_name> -> Settings -> API Keys.
+  #sentry_dsn: ''
+
+  # Sentry slow request logging.  Requests slower than the threshold
+  # indicated below will be sent as events to the configured Sentry
+  # server (above, sentry_dsn).  A value of '0' is disabled.  For
+  # example, you would set this to .005 to log all queries taking longer
+  # than 5 milliseconds.
+  #sentry_sloreq_threshold: 0.0
+
+  # Log to statsd Statsd is an external statistics aggregator
+  # (https://github.com/etsy/statsd) Enabling the following options will
+  # cause galaxy to log request timing and other statistics to the
+  # configured statsd instance.  The statsd_prefix is useful if you are
+  # running multiple Galaxy instances and want to segment statistics
+  # between them within the same aggregator.
+  #statsd_host: null
+
+  # Log to statsd Statsd is an external statistics aggregator
+  # (https://github.com/etsy/statsd) Enabling the following options will
+  # cause galaxy to log request timing and other statistics to the
+  # configured statsd instance.  The statsd_prefix is useful if you are
+  # running multiple Galaxy instances and want to segment statistics
+  # between them within the same aggregator.
+  #statsd_port: 8125
+
+  # Log to statsd Statsd is an external statistics aggregator
+  # (https://github.com/etsy/statsd) Enabling the following options will
+  # cause galaxy to log request timing and other statistics to the
+  # configured statsd instance.  The statsd_prefix is useful if you are
+  # running multiple Galaxy instances and want to segment statistics
+  # between them within the same aggregator.
+  #statsd_prefix: galaxy
+
+  # If you are using telegraf to collect these metrics and then sending
+  # them to InfluxDB, Galaxy can provide more nicely tagged metrics.
+  # Instead of sending prefix + dot-separated-path, Galaxy will send
+  # prefix with a tag path set to the page url
+  #statsd_influxdb: false
+
+  # Add an option to the library upload form which allows administrators
+  # to upload a directory of files.
+  #library_import_dir: ''
+
+  # Add an option to the library upload form which allows authorized
+  # non-administrators to upload a directory of files.  The configured
+  # directory must contain sub-directories named the same as the non-
+  # admin user's Galaxy login ( email ).  The non-admin user is
+  # restricted to uploading files or sub-directories of files contained
+  # in their directory.
+  #user_library_import_dir: ''
+
+  # If user_library_import_dir is set, this option will auto create a
+  # library import directory for every user (based on their email) upon
+  # login.
+  #user_library_import_dir_auto_creation: false
+
+  # For security reasons, users may not import any files that actually
+  # lie outside of their `user_library_import_dir` (e.g. using symbolic
+  # links). A list of directories can be allowed by setting the
+  # following option (the list is comma-separated). Be aware that *any*
+  # user with library import permissions can import from anywhere in
+  # these directories (assuming they are able to create symlinks to
+  # them).
+  #user_library_import_symlink_whitelist: ''
+
+  # In conjunction or alternatively, Galaxy can restrict user library
+  # imports to those files that the user can read (by checking basic
+  # unix permissions). For this to work, the username has to match the
+  # username on the filesystem.
+  #user_library_import_check_permissions: false
+
+  # Allow admins to paste filesystem paths during upload. For libraries
+  # this 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 implication that this
+  # will give Galaxy Admins access to anything your Galaxy user has
+  # access to.
+  #allow_path_paste: false
+
+  # Users may choose to download multiple files from a library in an
+  # archive.  By default, Galaxy allows users to select from a few
+  # different archive formats 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: null
+
+  # Some sequencer integration features in beta allow you to
+  # automatically transfer datasets.  This is done using a lightweight
+  # transfer manager which runs outside of Galaxy (but is spawned by it
+  # automatically).  Galaxy will communicate with this manager over the
+  # port specified here.
+  #transfer_manager_port: 8163
+
+  # Boosts are used to customize this instance's toolbox search. The
+  # higher the boost, the more importance the scoring algorithm gives to
+  # the given field.  Section refers to the tool group in the tool
+  # panel.  Rest of the fields are tool's attributes.
+  #tool_name_boost: 9.0
+
+  # Boosts are used to customize this instance's toolbox search. The
+  # higher the boost, the more importance the scoring algorithm gives to
+  # the given field.  Section refers to the tool group in the tool
+  # panel.  Rest of the fields are tool's attributes.
+  #tool_section_boost: 3.0
+
+  # Boosts are used to customize this instance's toolbox search. The
+  # higher the boost, the more importance the scoring algorithm gives to
+  # the given field.  Section refers to the tool group in the tool
+  # panel.  Rest of the fields are tool's attributes.
+  #tool_description_boost: 2.0
+
+  # Boosts are used to customize this instance's toolbox search. The
+  # higher the boost, the more importance the scoring algorithm gives to
+  # the given field.  Section refers to the tool group in the tool
+  # panel.  Rest of the fields are tool's attributes.
+  #tool_label_boost: 1.0
+
+  # Boosts are used to customize this instance's toolbox search. The
+  # higher the boost, the more importance the scoring algorithm gives to
+  # the given field.  Section refers to the tool group in the tool
+  # panel.  Rest of the fields are tool's attributes.
+  #tool_stub_boost: 5.0
+
+  # Boosts are used to customize this instance's toolbox search. The
+  # higher the boost, the more importance the scoring algorithm gives to
+  # the given field.  Section refers to the tool group in the tool
+  # panel.  Rest of the fields are tool's attributes.
+  #tool_help_boost: 0.5
+
+  # Limits the number of results in toolbox search.  Can be used to
+  # tweak how many results will appear.
+  #tool_search_limit: 20
+
+  # Enable/ disable Ngram-search for tools. It makes tool search results
+  # tolerant for spelling mistakes in the query by dividing the query
+  # into multiple ngrams and search for each ngram
+  #tool_enable_ngram_search: false
+
+  # Set minimum size of ngrams
+  #tool_ngram_minsize: 3
+
+  # Set maximum size of ngrams
+  #tool_ngram_maxsize: 4
+
+  # Set tool test data directory. The test framework sets this value to
+  # 'test-data,https://github.com/galaxyproject/galaxy-test-data.git'
+  # which will cause Galaxy to clone down extra test data on the fly for
+  # certain tools distributed with Galaxy but this is likely not
+  # appropriate for production systems. Instead one can simply clone
+  # that repository directly and specify a path here instead of a Git
+  # HTTP repository.
+  #tool_test_data_directories: test-data
+
+  # Galaxy encodes various internal values when these values will be
+  # output in some format (for example, in a URL or cookie).  You should
+  # set a key to be used by the algorithm that encodes and decodes these
+  # values. It can be any string with a length between 5 and 56 bytes.
+  # One simple way to generate a value for this is with the shell
+  # command:   python -c 'from __future__ import print_function; 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 Apache).  The upstream proxy should set a REMOTE_USER
+  # header in the request. Enabling remote user disables regular logins.
+  # For more information, see: https://docs.galaxyproject.org/en/master/
+  # admin/special_topics/apache.html
+  #use_remote_user: false
+
+  # If use_remote_user is enabled and your external authentication
+  # method just returns bare usernames, set a default mail domain to be
+  # appended to usernames, to become your Galaxy usernames (email
+  # addresses).
+  #remote_user_maildomain: ''
+
+  # If use_remote_user is enabled, the header that the upstream proxy
+  # provides the remote username in defaults to HTTP_REMOTE_USER (the
+  # 'HTTP_' is prepended by WSGI).  This option allows you to change the
+  # header.  Note, you still need to prepend 'HTTP_' to the header in
+  # this option, but your proxy server should *not* include 'HTTP_' at
+  # the beginning of the header name.
+  #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 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 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 users out.
+  #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.
+  #normalize_remote_user_email: false
+
+  # If an e-mail address is specified here, it will hijack remote user
+  # mechanics (``use_remote_user``) and have the webapp inject a single
+  # fixed user. This has the effect of turning Galaxy into a single user
+  # application with no login or external proxy required. Such
+  # applications should not be exposed to the world.
+  #single_user: null
+
+  # Administrative users - set this to a comma-separated list of valid
+  # Galaxy users (email addresses).  These users will have access to the
+  # Admin section of the server, and will have access to create users,
+  # groups, roles, libraries, and more.  For more information, see:
+  # https://galaxyproject.org/admin/
+  # admin_users: [e-mail], [e-mail]
+
+  # Force everyone to log in (disable anonymous access).
+  # require_login: true
+
+  # Show the site's welcome page (see welcome_url) alongside the login
+  # page (even if require_login is True)
+  # show_welcome_with_login: true
+
+  # Allow unregistered users to create new accounts (otherwise, they
+  # will have to be created by an admin).
+  # allow_user_creation: true
+
+  # Allow administrators to delete accounts.
+  # allow_user_deletion: true
+
+  # Allow administrators to log in as other users (useful for debugging)
+  #allow_user_impersonation: false
+
+  # When using LDAP for authentication, allow administrators to pre-
+  # populate users using an additional form on 'Create new user'
+  #show_user_prepopulate_form: false
+
+  # Allow users to remove their datasets from disk immediately
+  # (otherwise, datasets will be removed after a time period specified
+  # 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
+  # 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
+  # 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.
+  #expose_user_name: false
+
+  # 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.
+  #expose_user_email: false
+
+  # Whitelist for local network addresses for "Upload from URL" dialog.
+  # By default, Galaxy will deny access to the local network address
+  # space, to prevent users making requests to services which the
+  # administrator did not intend to expose. Previously, you could
+  # request any network service that Galaxy might have had access to,
+  # even if the user could not normally access it. It should be a comma
+  # separated list of IP addresses or IP address/mask, e.g.
+  # 10.10.10.10,10.0.1.0/24,fd00::/8
+  #fetch_url_whitelist: null
+
+  # Enables GDPR Compliance mode. This makes several changes to the way
+  # Galaxy logs and exposes data externally such as removing emails and
+  # usernames from logs and bug reports. It also causes the delete user
+  # admin action to permanently redact their username and password, but
+  # not to delete data associated with the account as this is not
+  # currently easily implementable.  You are responsible for removing
+  # personal data from backups.  This forces expose_user_email and
+  # expose_user_name to be false, and forces user_deletion to be true to
+  # support the right to erasure.  Please read the GDPR section under
+  # the special topics area of the admin documentation.
+  #enable_beta_gdpr: false
+
+  # Enable the new interface for installing tools from Tool Shed via the
+  # API. Admin menu will list both if enabled.
+  #enable_beta_ts_api_install: true
+
+  # Enable the new container interface for Interactive Environments
+  #enable_beta_containers_interface: false
+
+  # Set the following to a number of threads greater than 1 to spawn a
+  # Python task queue for dealing with large tool submissions (either
+  # through the tool form or as part of an individual workflow step
+  # across large collection). This affects workflow scheduling and web
+  # processes, not job handlers. This is a beta option and should not be
+  # used in production.
+  #tool_submission_burst_threads: 1
+
+  # If tool_submission_burst_threads is set to a number greater than 1,
+  # this is the number of jobs to schedule at which the task queue will
+  # be created.
+  #tool_submission_burst_at: 10
+
+  # Enable beta workflow modules that should not yet be considered part
+  # of Galaxy's stable API.
+  #enable_beta_workflow_modules: false
+
+  # Following options only apply to workflows scheduled using the legacy
+  # workflow run API (running workflows via a POST to /api/workflows).
+  # Force usage of Galaxy's beta workflow scheduler under certain
+  # circumstances - this workflow scheduling forces Galaxy to schedule
+  # workflows in the background so initial submission of the workflows
+  # is significantly sped up. This does however force the user to
+  # refresh their history manually to see newly scheduled steps (for
+  # "normal" workflows - steps are still scheduled far in advance of
+  # them being queued and scheduling here doesn't refer to actual
+  # cluster job scheduling). Workflows containing more than the
+  # specified number of steps will always use the Galaxy's beta workflow
+  # scheduling.
+  #force_beta_workflow_scheduled_min_steps: 250
+
+  # Following options only apply to workflows scheduled using the legacy
+  # workflow run API (running workflows via a POST to /api/workflows).
+  # Force usage of Galaxy's beta workflow scheduler under certain
+  # circumstances - this workflow scheduling forces Galaxy to schedule
+  # workflows in the background so initial submission of the workflows
+  # is significantly sped up. This does however force the user to
+  # refresh their history manually to see newly scheduled steps (for
+  # "normal" workflows - steps are still scheduled far in advance of
+  # them being queued and scheduling here doesn't refer to actual
+  # cluster job scheduling). Workflows containing more than the
+  # specified number of steps will always use the Galaxy's beta workflow
+  # scheduling. Switch to using Galaxy's beta workflow scheduling for
+  # all workflows involving collections.
+  #force_beta_workflow_scheduled_for_collections: false
+
+  # If multiple job handlers are enabled, allow Galaxy to schedule
+  # workflow invocations in multiple handlers simultaneously. This is
+  # discouraged because it results in a less predictable order of
+  # workflow datasets within in histories.
+  #parallelize_workflow_scheduling_within_histories: false
+
+  # This is the maximum amount of time a workflow invocation may stay in
+  # an active scheduling state in seconds. Set to -1 to disable this
+  # maximum and allow any workflow invocation to schedule indefinitely.
+  # The default corresponds to 1 month.
+  #maximum_workflow_invocation_duration: 2678400
+
+  # Specify a maximum number of jobs that any given workflow scheduling
+  # iteration can create. Set this to a positive integer to prevent
+  # large collection jobs in a workflow from preventing other jobs from
+  # executing. This may also mitigate memory issues associated with
+  # scheduling workflows at the expense of increased total DB traffic
+  # because model objects are expunged from the SQL alchemy session
+  # between workflow invocation scheduling iterations. Set to -1 to
+  # disable any such maximum (the default).
+  #maximum_workflow_jobs_per_scheduling_iteration: -1
+
+  # Force serial scheduling of workflows within the context of a
+  # particular history
+  #history_local_serial_workflow_scheduling: false
+
+  # Enable authentication via OpenID.  Allows users to log in to their
+  # Galaxy account by authenticating with an OpenID provider.
+  #enable_openid: false
+
+  # If OpenID is enabled, this configuration file specifies providers to
+  # use. Falls back to the .sample variant in config if default does not
+  # exist.
+  #openid_config_file: config/openid_conf.xml
+
+  # If OpenID is enabled, consumer cache directory to use.
+  #openid_consumer_cache_path: database/openid_consumer_cache
+
+  # Enables and disables OpenID Connect (OIDC) support.
+  #enable_oidc: false
+
+  # Sets the path to OIDC configuration file.
+  #oidc_config_file: config/oidc_config.xml
+
+  # Sets the path to OIDC backends configuration file.
+  #oidc_backends_config_file: config/oidc_backends_config.xml
+
+  # XML config file that allows the use of different authentication
+  # providers (e.g. LDAP) instead or in addition to local authentication
+  # (.sample is used if default does not exist).
+  #auth_config_file: config/auth_conf.xml
+
+  # Optional list of email addresses of API users who can make calls on
+  # behalf of other users.
+  #api_allow_run_as: ''
+
+  # 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.
+  #master_api_key: changethis
+
+  # Enable tool tags (associating tools with tags).  This has its own
+  # option since its implementation has a few performance implications
+  # on startup for large servers.
+  #enable_tool_tags: false
+
+  # 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,
+  # the most recently added compatible item in the history will be used
+  # for each "Set at Runtime" input, independent of others in the
+  # Workflow
+  #enable_unique_workflow_defaults: false
+
+  # The URL to the myExperiment instance being used (omit scheme but
+  # include port)
+  #myexperiment_url: 'www.myexperiment.org:80'
+
+  # Enable Galaxy's "Upload via FTP" interface.  You'll need to install
+  # and configure an FTP server (we've used ProFTPd since it can use
+  # Galaxy's database for authentication) and set the following two
+  # options. This should point to a directory containing subdirectories
+  # matching users' identifier (defaults to e-mail), where Galaxy will
+  # look for files.
+  #ftp_upload_dir: ''
+
+  # This should be the hostname of your FTP server, which will be
+  # provided to users in the help text.
+  #ftp_upload_site: ''
+
+  # User attribute to use as subdirectory in calculating default
+  # ftp_upload_dir pattern. By default this will be email so a user's
+  # FTP upload directory will be ${ftp_upload_dir}/${user.email}. Can
+  # set this to other attributes such as id or username though.
+  #ftp_upload_dir_identifier: email
+
+  # Python string template used to determine an FTP upload directory for
+  # 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.
+  #ftp_upload_purge: true
+
+  # Enable enforcement of quotas.  Quotas can be set from the Admin
+  # interface.
+  #enable_quotas: false
+
+  # This option allows users to see the full path of datasets via the
+  # "View Details" option in the history. This option also exposes the
+  # command line to non-administrative users. Administrators can always
+  # see dataset paths.
+  #expose_dataset_path: false
+
+  # This option allows users to see the job metrics (except for
+  # environment variables).
+  #expose_potentially_sensitive_job_metrics: false
+
+  # Enable the API for sample tracking
+  #enable_legacy_sample_tracking_api: false
+
+  # Allow non-admin users to view available Data Manager options.
+  #enable_data_manager_user_view: false
+
+  # 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.
+  #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
+
+  # To increase performance of job execution and the web interface, you
+  # can separate Galaxy into multiple processes.  There are more than
+  # one way to do this, and they are explained in detail in the
+  # documentation:
+  # https://docs.galaxyproject.org/en/master/admin/scaling.html  By
+  # default, Galaxy manages and executes jobs from within a single
+  # process and notifies itself of new jobs via in-memory queues.  Jobs
+  # are run locally on the system on which Galaxy is started.  Advanced
+  # job running capabilities can be configured through the job
+  # configuration file.
+  #job_config_file: config/job_conf.xml
+
+  # 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
+  # job_conf.xml. For simple deployments of Galaxy though, the following
+  # attribute can define resubmission conditions for all job
+  # destinations. If any job destination defines even one resubmission
+  # condition explicitly in job_conf.xml - the condition described by
+  # this option will not apply to that destination. For instance, the
+  # condition: 'attempt < 3 and unknown_error and (time_running < 300 or
+  # time_since_queued < 300)' would retry up to two times jobs that
+  # didn't fail due to detected memory or walltime limits but did fail
+  # quickly (either while queueing or running). The commented out
+  # default below results in no default job resubmission condition,
+  # failing jobs are just failed outright.
+  #default_job_resubmission_condition: null
+
+  # In multiprocess configurations, notification between processes about
+  # new jobs must be done via the database.  In single process
+  # configurations, this can be done in memory, which is a bit quicker.
+  #track_jobs_in_database: true
+
+  # 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
+
+  # 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.
+  #local_task_queue_workers: 2
+
+  # Enable job recovery (if Galaxy is restarted while cluster jobs are
+  # running, it can "recover" them when it starts).  This is not safe to
+  # use if you are running more than one Galaxy server using the same
+  # database.
+  #enable_job_recovery: true
+
+  # 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 option to retry externally,
+  # or set metadata manually (when possible).
+  #retry_metadata_internally: true
+
+  # Very large metadata values can cause Galaxy crashes.  This will
+  # allow limiting the maximum metadata key size (in bytes used in
+  # memory, not the end result database value size) Galaxy will attempt
+  # to save with a dataset.  Use 0 to disable this feature.  The default
+  # is 5MB, but as low as 1MB seems to be a reasonable size.
+  #max_metadata_value_size: 5242880
+
+  # This option will override tool output paths to write outputs to the
+  # job working directory (instead of to the file_path) and the job
+  # manager will move the outputs to their proper place in the dataset
+  # directory on the Galaxy server after the job completes. This is
+  # necessary (for example) if jobs run on a cluster and datasets can
+  # not be created by the user running the jobs (e.g. if the filesystem
+  # is mounted read-only or the jobs are run by a different user than
+  # the galaxy user).
+  #outputs_to_working_directory: false
+
+  # If your network filesystem's caching prevents the Galaxy server from
+  # seeing the job's stdout and stderr files when it completes, you can
+  # retry reading these files.  The job runner will retry the number of
+  # times specified below, waiting 1 second between tries.  For NFS, you
+  # may want to try the -noac mount option (Linux) or -actimeo=0
+  # (Solaris).
+  #retry_job_output_collection: 0
+
+  # In the past Galaxy would preserve its Python environment when
+  # running jobs ( and still does for internal tools packaged with
+  # Galaxy). This behavior exposes Galaxy internals to tools and could
+  # result in problems when activating Python environments for tools
+  # (such as with Conda packaging). The default legacy_only will
+  # restrict this behavior to tools identified by the Galaxy team as
+  # requiring this environment. Set this to "always" to restore the
+  # previous behavior (and potentially break Conda dependency resolution
+  # for many tools). Set this to legacy_and_local to preserve the
+  # environment for legacy tools and locally managed tools (this might
+  # be useful for instance if you are installing software into Galaxy's
+  # virtualenv for tool development).
+  #preserve_python_environment: legacy_only
+
+  # Clean up various bits of jobs left on the filesystem after
+  # completion.  These bits include the job working directory, external
+  # metadata temporary files, and DRM stdout and stderr files (if using
+  # a DRM).  Possible values are: always, onsuccess, never
+  #cleanup_job: always
+
+  # When running DRMAA jobs as the Galaxy user
+  # (https://docs.galaxyproject.org/en/master/admin/cluster.html
+  # #submitting-jobs-as-the-real-user) this script is used to run the
+  # job script Galaxy generates for a tool execution.
+  #drmaa_external_runjob_script: sudo -E scripts/drmaa_external_runner.py --assign_all_groups
+
+  # When running DRMAA jobs as the Galaxy user
+  # (https://docs.galaxyproject.org/en/master/admin/cluster.html
+  # #submitting-jobs-as-the-real-user) this script is used to kill such
+  # jobs by Galaxy (e.g. if the user cancels the job).
+  #drmaa_external_killjob_script: sudo -E scripts/drmaa_external_killer.py
+
+  # When running DRMAA jobs as the Galaxy user
+  # (https://docs.galaxyproject.org/en/master/admin/cluster.html
+  # #submitting-jobs-as-the-real-user) this script is used transfer
+  # permissions back and forth between the Galaxy user and the user that
+  # is running the job.
+  #external_chown_script: sudo -E scripts/external_chown_script.py
+
+  # When running DRMAA jobs as the Galaxy user
+  # (https://docs.galaxyproject.org/en/master/admin/cluster.html
+  # #submitting-jobs-as-the-real-user) Galaxy can extract the user name
+  # from the email address (actually the local-part before the @) or the
+  # username which are both stored in the Galaxy data base. The latter
+  # option is particularly useful for installations that get the
+  # authentication from LDAP. Also, Galaxy can accept the name of a
+  # common system user (eg. galaxy_worker) who can run every job being
+  # submitted. This user should not be the same user running the galaxy
+  # system. Possible values are user_email (default), username or
+  # <common_system_user>
+  #real_system_username: user_email
+
+  # File to source to set up the environment when running jobs.  By
+  # default, the environment in which the Galaxy server starts is used
+  # when running jobs locally, and the environment set up per the DRM's
+  # submission method and policy is used when running jobs on a cluster
+  # (try testing with `qsub` on the command line).
+  # environment_setup_file can be set to the path of a file on the
+  # cluster that should be sourced by the user to set up the environment
+  # prior to running tools.  This can be especially useful for running
+  # jobs as the actual user, to remove the need to configure each user's
+  # environment individually.
+  #environment_setup_file: ''
+
+  # 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.
+  #job_resource_params_file: config/job_resource_params_conf.xml
+
+  # Similar to the above parameter, workflows can describe parameters
+  # used to influence scheduling of jobs within the workflow. This
+  # requires both a description of the fields available (which defaults
+  # to the definitions in job_resource_params_file if not set).
+  #workflow_resource_params_file: config/workflow_resource_params_conf.xml
+
+  # This parameter describes how to map users and workflows to a set of
+  # workflow resource parameter to present (typically input IDs from
+  # workflow_resource_params_file). If this this is a function reference
+  # it will be passed various inputs (workflow model object and user)
+  # and it should produce a list of input IDs. If it is a path it is
+  # expected to an XML or YAML file describing how to map group names to
+  # parameter descriptions (additional types of mappings via these files
+  # could be implemented but haven't yet - for instance using workflow
+  # tags to do the mapping).
+  #workflow_resource_params_mapper: config/workflow_resource_mapper_conf.yml
+
+  # If using job concurrency limits (configured in job_config_file),
+  # 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
+  # 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.
+  #cache_user_job_count: false
+
+  # Define toolbox filters (https://galaxyproject.org/user-defined-
+  # toolbox-filters/) that admins may use to restrict the tools to
+  # display.
+  #tool_filters: null
+
+  # Define toolbox filters (https://galaxyproject.org/user-defined-
+  # toolbox-filters/) that admins may use to restrict the tool labels to
+  # display.
+  #tool_label_filters: null
+
+  # Define toolbox filters (https://galaxyproject.org/user-defined-
+  # toolbox-filters/) that admins may use to restrict the tool sections
+  # to display.
+  #tool_section_filters: null
+
+  # Define toolbox filters (https://galaxyproject.org/user-defined-
+  # toolbox-filters/) that users may use to restrict the tools to
+  # display.
+  #user_tool_filters: 'examples:restrict_upload_to_admins, examples:restrict_encode'
+
+  # Define toolbox filters (https://galaxyproject.org/user-defined-
+  # toolbox-filters/) that users may use to restrict the tool sections
+  # to display.
+  #user_tool_section_filters: 'examples:restrict_text'
+
+  # Define toolbox filters (https://galaxyproject.org/user-defined-
+  # toolbox-filters/) that users may use to restrict the tool labels to
+  # display.
+  #user_tool_label_filters: 'examples:restrict_upload_to_admins, examples:restrict_encode'
+
+  # The base module(s) that are searched for modules for toolbox
+  # filtering (https://galaxyproject.org/user-defined-toolbox-filters/)
+  # functions.
+  #toolbox_filter_base_modules: 'galaxy.tools.toolbox.filters,galaxy.tools.filters'
+
+  # Galaxy uses AMQP internally for communicating between processes.
+  # For example, when reloading the toolbox or locking job execution,
+  # the process that handled that particular request will tell all
+  # others to also reload, lock jobs, etc. For connection examples, see
+  # http://docs.celeryproject.org/projects/kombu/en/latest/userguide/con
+  # nections.html  Without specifying anything here, galaxy will first
+  # attempt to use your specified database_connection above.  If that's
+  # not specified either, Galaxy will automatically create and use a
+  # separate sqlite database located in your <galaxy>/database folder
+  # (indicated in the commented out line below).
+  #amqp_internal_connection: 'sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE'
+
+  # Galaxy real time communication server settings
+  #enable_communication_server: false
+
+  # Galaxy real time communication server settings
+  #communication_server_host: 'http://localhost'
+
+  # Galaxy real time communication server settings
+  #communication_server_port: 7070
+
+  # persistent_communication_rooms is a comma-separated list of rooms
+  # that should be always available.
+  #persistent_communication_rooms: null
+
+  # Allow disabling pbkdf2 hashing of passwords for legacy situations.
+  # This should normally be left enabled unless there is a specific
+  # reason to disable it.
+  #use_pbkdf2: true
\ No newline at end of file

--- a/pipe-t.R	Wed May 15 06:54:59 2019 -0400
+++ b/pipe-t.R	Thu May 16 10:34:26 2019 -0400
@@ -569,7 +569,8 @@
   height = 10*300,
   res = 300,            # 300 pixels per inch
   pointsize = 8)
-  plotCtBoxes(xFilter, stratify=NULL, xlab = "Samples", ylab="Ct", names=as.character(seq(1, ncol(xFilter), 1)))       # smaller font size
+ par(mar = c(8, 8,8, 8)) 
+  plotCtBoxes(xFilter, cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="Ct", names=as.character(seq(1, ncol(xFilter), 1)))       # smaller font size
 dev.off()
 
 #write.table(exprs(xFilter), file=x, quote=FALSE,  row.names=TRUE, col.names=TRUE,sep = "\t")
@@ -724,22 +725,6 @@
 	# Return the normalised object
 	q
 }
-#library(NormqPCR)
-
-#delete.na <- function(DF, n=0) {
- # DF[rowSums(is.na(DF)) <= n,]
-#}
-
-#user_number=5
-#genorm <- selectHKs(t(delete.na(as.matrix(exprs(xGlico)),0)), method = "geNorm", Symbols = rownames(as.matrix(delete.na(exprs(xGlico),0))), minNrHK = as.numeric(user_number), log = TRUE)
-#genorm
-#normfinder <- selectHKs(as.matrix(t(delete.na(exprs(xGlico),0))), group= files$Treatment , method = "NormFinder", Symbols =rownames(as.matrix(delete.na(exprs(xGlico),0))), minNrHK = as.numeric(user_number), log = TRUE)
-#normfinder
-#intersection= intersect(normfinder$ranking, genorm$ranking[1:as.numeric(user_number)])
-
-#cat("\n GeNorm and NormFinder transcripts selected as housekeeping for normalization! \n")
-#intersection
-#dnorm <- normalizeCtData(xGlico , norm="deltaCt", deltaCt.genes=as.vector(intersection)) 
 
 switch(normalizationMethod,
     "deltaCt"={
@@ -783,29 +768,11 @@
     stop("Enter something that switches me!")
 )
 
-  #if (normalizationMethod=="deltaCt") {
-#normalize CT data
-
-#normalizedDataset <- normalizeCtDataDav(xFilter, norm="deltaCt",  deltaCt.genes =explode(normalizers, sep = ","))
-#} else {
-#normalizedDataset <- normalizeCtDataDav(xFilter, norm=normalizationMethod)
-
-#}
+  
 cat("\n Data normalized correctly! \n")
 write.table(exprs(normalizedDataset), file=outputNorm, quote=FALSE,  row.names=TRUE, col.names=TRUE,sep = "\t")
 
 
-#normalizedDataset
-####################################################################################################################
-#Check noise reduction by empirical cumulative distribution
-
-#X = rnorm(100) # X is a sample of 100 normally distributed random variables
-# P = ecdf(X)    # P is a function giving the empirical CDF of X
-#Y = rnorm(1000) # X is a sample of 100 normally distributed random variables
-# PY = ecdf(Y)
-#plot℗
-
-#lines(PY)
 png(outputECDF,    # create PNG for the heat map
   width = 10*300,        # 5 x 300 pixels
   height = 10*300,
@@ -828,8 +795,8 @@
 PY = ecdf(gm)
 
 plot_colors <- c(rgb(r=0.0,g=0.0,b=0.9), "red", "forestgreen",rgb(r=0.0,g=0.0,b=0.0),rgb(r=0.5,g=0.0,b=0.3),rgb(r=0.0,g=0.4,b=0.4))
-
-plot(P,col=plot_colors[1],xlim=c(0.0,600),  ylim=c(0.0,1),xaxp = c(0.0, 600, 6),yaxp = c(0.0, 1, 10), cex=1.3, lwd=5, main=NULL,xlab="CV(%)",ylab="Empirical Cumulative Distribution")
+par(mar = c(8, 8,8, 8)) # Set the margin on all sides to 8
+plot(P,cex.lab=3, cex.axis = 2,col=plot_colors[1],xlim=c(0.0,600),  ylim=c(0.0,1),xaxp = c(0.0, 600, 6),yaxp = c(0.0, 1, 10), cex=1.3, lwd=5, main=paste("p-value=", formatC(ks.test(vec,gm)$p.value, format = "e", digits = 2)),xlab="CV(%)",ylab="Empirical Cumulative Distribution")
 lines(PY, lwd=5, col=plot_colors[6],cex=1.3)
 legend("bottomright", c("not normalized", "normalized"), cex=1.3, col=c(plot_colors[1],plot_colors[6]), lwd=c(5,5));
 dev.off()
@@ -844,7 +811,8 @@
   height = 10*300,
   res = 300,            # 300 pixels per inch
   pointsize = 8)
-  plotCtBoxes(normalizedDataset, stratify=NULL, xlab = "Samples", ylab="DeltaCt", names=as.character(seq(1, ncol(normalizedDataset), 1)))       # smaller font size
+  par(mar = c(8, 8,8, 8))
+  plotCtBoxes(normalizedDataset, cex.lab=3, cex.axis = 2,stratify=NULL, xlab = "Samples", ylab="DeltaCt", names=as.character(seq(1, ncol(normalizedDataset), 1)))       # smaller font size
 dev.off()
 
 ################################################## Filtering based on number of NAs##################################################