app.yml.sample

## Directory to stage files to. This should likely be updated to point
## to an absolute path, such as /tmp/pulsar_staging or C:\\pulsar_staging
#staging_directory: files/staging

## Configure one or more named managers (more information on configuring managers
## can be found at http://pulsar.readthedocs.org/en/latest/job_managers.html).
#managers:
#  _default_:
#    type: queued_python
#    num_concurrent_jobs: 1


## Mode to create job releated directories with. If unset
## will just use 0777 with umask mask applied.
#job_directory_mode: 0777

## Private token that must be sent as part of the request to
## authorize use. If security is important, please use this in
## combination with SSL.
#private_token: changemeinproduction

## Pulsar stores information about active jobs in the following directory - if
## user the Pulsar runs as cannot write to the Pulsar root directory this
## should be updated to point to some directory which it can write to. Set this
## value to __none__ to disable persisting jobs all together.
#persistence_directory: files/persisted_data

## How are ids assigned. galaxy (default) just passes through ids as
## is. Setting this uuid assigns each job a UUID, this is strongly
## encouraged if multiple Galaxy servers are targetting one Pulsar server.
#assign_ids: uuid

## Pulsar-equivalent of Galaxy's tool_dependency_dir. The default directory
## used by tool dependency resolves to find dependency scripts. Used
## if Galaxy configures remote dependency resolution.
#tool_dependency_dir: dependencies

## Set up tool dependency resolvers. See Galaxy dependency resolver
## documentation:
##   https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
## and `dependency_resolution` option documentation in the config schema:
##   https://github.com/galaxyproject/galaxy/blob/release_21.05/lib/galaxy/webapps/galaxy/config_schema.yml
## for more information on dependency resolvers, options, and exact syntax.
#dependency_resolution:
#  resolvers:
#    - type: conda
#      auto_init: true
#      auto_install: false
#      prefix: dependencies/_conda

## Alternatively, you can specify dependency resolvers in a separate XML or YAML
## file. See Galaxy documentation for the syntax. If
## dependency_resolution.resolvers is set above, it overrides the configuration
## in this file (if present). If dependency_resolution.resolvers is unset and
## dependency_resolvers_conf.xml is present, it will be used unless the path is
## overridden by this option.
#dependency_resolvers_config_file: dependency_resolvers_conf.xml

## These options configure the conda tool dependency resolver at the global
## level and correspond to the non-`conda_*` parameters in the dependency
## resolvers config.
##
## Automatically install Conda on startup if it is not already installed.
#conda_auto_init: true
## Automatically install missing tool dependencies at tool runtime.
#conda_auto_install: false
## Root of Conda installation.
#conda_prefix: dependencies/_conda

## Comma separated list of paths to toolbox files. If this is set, Pulsar
## will use the information contained in the tools to lock down what
## the Pulsar can execute. This absolutely *SHOULD* be enabled if the Pulsar
## server is being opened to the world. See the documentation
## (pulsar.readthedocs.org) for more information about securing Pulsar.
#tool_config_files: toolbox/conf.xml

## Setup job metrics file. See Galaxy documentaiton for more
## information on job metrics. If job_metrics_conf.xml is present,
## it will be used unless overridden by this option.
#job_metrics_config_file: job_metrics_conf.xml

## Bind the Pulsar to an AMQP endpoint. Ensure kombu
## Python library is available and start the Pulsar normally.
#message_queue_url: amqp://guest:guest@localhost:5672//

## Pulsar loops over waiting for queue messages for a short time before checking
## to see if it has been instructed to shut down. By default this is 0.2
## seconds. This value is used as the value of the 'timeout' parameter to
## kombu.Connection's drain_events() method.
#amqp_consumer_timeout: 0.2

## publishing messages to the queue may hang if the connection becomes invalid.
## this value is used as the timeout argument to the producer.publish function.
#amqp_publish_timeout: 2.0

# AMQP does not guarantee that a published message is received by the AMQP
# server, so Pulsar can request that the consumer acknowledge messages and will
# resend them if acknowledgement is not received after a configurable timeout
# (in seconds).
#amqp_acknowledge: false
#amqp_ack_republish_time: 30

## The AMQP client can provide an SSL client certificate (e.g. for
## validation), the following options configure that certificate
## (see for reference:
##   http://kombu.readthedocs.org/en/latest/reference/kombu.connection.html
## ). If you simply want to use SSL but not use/validate a client
## cert, just use the ?ssl=1 query on the amqp URL instead.
#amqp_connect_ssl_ca_certs: /path/to/cacert.pem
#amqp_connect_ssl_keyfile: /path/to/key.pem
#amqp_connect_ssl_certfile: /path/to/cert.pem
#amqp_connect_ssl_cert_reqs: cert_required

## AMQP Reconnection Parameters. Control if, and how often messages are re-sent
##if they fail
# Comments taken from http://kombu.readthedocs.org/en/latest/reference/kombu.connection.html#kombu.connection.Connection.ensure
#amqp_publish_retry: True
## Maximum number of times to retry. If this limit is exceeded the connection error will be re-raised.
#amqp_publish_retry_max_retries: 5
## The number of seconds we start sleeping for.
#amqp_publish_retry_interval_start: 10
## How many seconds added to the interval for each retry.
#amqp_publish_retry_interval_step: 10
## Maximum number of seconds to sleep between each retry.
#amqp_publish_retry_interval_max: 60


## configure user authentication/authorization plugins
## parameters depend on auth type. Authentication plugin should return a username
## and authorization plugin should authorize this user
#user_auth:
#  authentication:
#    - type: oidc
#      oidc_jwks_url: https://login.microsoftonline.com/xxx/discovery/v2.0/keys
#      oidc_provider: azure
#      oidc_username_in_token: preferred_username
#      oidc_username_template: *.
#  authorization:
#    - type: userlist
#      userlist_allowed_users:
#        - xxx

## *Experimental*. Enable file caching by specifing a directory here. 
## Directory used to store incoming file cache. It works fine for HTTP
## transfer, have not tested with staging by coping. Also there is no
## mechanism for expiring cache so it will grow unbounded without
## external clean up.
#file_cache_dir: cache

## 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: null

## Determines the minimum log level that will be sent as an event to
## Sentry. Possible values are DEBUG, INFO, WARNING, ERROR or CRITICAL.
##sentry_event_level: WARNING