galaxy/config/tool_destinations.yml.sample

# Dynamic Tool Destinations config has four main levels (or key properties) - tools,
# default_destination, users, and verbose.
#
# Under tools is where you put the IDs of the tools. Tool IDs must be
# distinct. In each tool is a list of rules, each of which contain rule-specific
# paremeters. Dynamic Tool Destination is set up to allow and fix a few light errors
# in the config, but it's best to follow the specified template.
#
# default_destination, the second key property, specifies which global destination
# to default to in case none of the rules apply.
#
# users, the third key property, can be used to assign a priority to a user. Three priorities
# are available low, med, and high. By default all users are assumed to be med priority. If
# a rule has priority destinations the user will be set to the destination which matches their priority
# or if their priority isn't available they will be matched to the next closest one.
#
# A fourth key property is verbose. When this is set to True, Dynamic Tool Destination
# gives much more descriptive output regarding the steps it's taking in mapping your tools to
# the appropriate destinations, including config validation and any potential errors found in the
# config.
#
# Note: Configurations can be validated with the following command:
#
#    python lib/galaxy/jobs/dynamic_tool_destination.py -c
#
# or
#
#    python lib/galaxy/jobs/dynamic_tool_destination.py -c /path/to/tool_destinations.yml
#
# The general template is as follows (note that this template
# does not use quote symbols), using spades and smalt as an example
# (spades for showing what each field is for, and smalt
# to give a fairly real-world example):
#
# Ex:
#
# tools:
#   spades:
#     rules:
#       - rule_type: what kind of rule is it?
#         nice_value: what kind of priority does this rule have over others?
#         destination: how should this tool be run?
#         lower_bound: what's the max file size?
#         upper_bound: what's the minimum file size?
#         users: #(optional) which users does this rule apply to
#           - user@example.com
#     default_destination: this tool-specific field is optional
#   smalt_map:
#     rules:
#       - rule_type: file_size
#         nice_value: 0
#         lower_bound: 0
#         upper_bound: 2 GB
#         destination: cluster_low_4
#       - rule_type: file_size
#         nice_value: 0
#         lower_bound: 2 GB
#         upper_bound: 4 GB
#         destination: cluster_low_8
#       - rule_type: file_size
#         nice_value: 0
#         lower_bound: 4 GB
#         upper_bound: Infinity
#         destination: cluster_low_16
#     default_destination: cluster_default
# users:
#   user_low@example.com:
#     priority: low
#   user_med@example.com:
#     priority: med
#   user_high@example.com:
#     priority: high
# default_destination: this global field is mandatory
# verbose: True
#
#
#
# Looking at this example, some things must be clarified: each entry in the list of
# rules per tool is specified by '-'. Per rule, regardless of rule type,
# the following fields are mandatory:
# rule_type, nice_value, and destination.
#
# Some of the other fields are mandatory only for specific rule types, which will be
# further discussed below.
#
# Starting with rule_type, there are currently 3 rule types: file_size, records,
# and arguments.
#
# file_size and records rules are based on how large the files are: if they fall
# within specified limits, then the rule is satisfied, and the tool may proceed
# with the appropriate destination.
#
# file_size and records rules have the following required parameters on top of the base
# mandatory parameters:
# upper_bound
# lower_bound
#
# Bounds are allowed to be specified in bytes (48000 for example) or a higher size unit,
# including the unit abbreviation (4 GB or 10 TB for example). Additionally, upper_bound
# is allowed to be Infinite; simply specify Infinite in order to do so.
#
# **The rule will allow the lower_bound, up to but not including the upper_bound
#
# The third rule_type is arguments, which has arguments as a mandatory parameter ontop of
# the base mandatory parameters. The arguments parameter is specified using the following
# template:
#
#
# arguments:
#   argument_name: the_argument
#
#
# A real world example is shown below:
#
#
# tools:
#   spades:
#     rules:
#       - rule_type: arguments
#         nice_value: -19
#         destination: fail
#         fail_message: Don't do that
#         arguments:
#           my_section:
#             my_condition:
#               careful: true
#     default_destination: cluster_low
# default_destination: cluster
# verbose: False
#
#
# Next up, nice_value is used for prioritizing rules over others in case two rules
# match. nice_value basically translates to, "the higher the nice_value, the 'nicer'
# the tool is about being picked last". So based off of that idea, a rule with a nice
# value of -5 is guaranteed to be picked over a rule with a nice value of 10. nice_value
# is allowed to go from -20 to 20. If two rules have the same nice value and both were
# satisfied, the first rule in the config file will be picked. In summary, first-come-
# first-serve basis unless nice_value overrides that.
#
#
# Finally, destination simply refers to the specific way the tool will run. Each
# destination ID refers to a specific configuration to run the tool with.
#
# Some rules may call for the job to fail if certain conditions are encountered. In
# this case, destination simply refers to 'fail'.
#
# For example, the following rule is set to fail the job if a file that is too large
# (more than 4GB) is encountered:
#
#
# tools:
#   spades:
#     rules:
#       - rule_type: file_size
#         nice_value: 0
#         destination: fail
#         fail_message: Data too large
#         lower_bound: 4 GB
#         upper_bound: Infinity
#
#
# As shown above, a rule with 'fail' as the destination requires an additional
# parameter, 'fail_message', which DynamicToolDestination uses to print a helpful error
# message to the user indicating why the job failed (showing up inside the job log in
# Galaxy's history panel).


tools:
  spades:
    rules:
      - rule_type: file_size
        nice_value: 0
        lower_bound: 0
        upper_bound: 10 MB
        fail_message: Too few reads for spades to work
        destination: fail
      - rule_type: file_size
        nice_value: 0
        lower_bound: 10 MB
        upper_bound: 2 GB
        destination:
          priority:
            low: slurm_low_24
            med: slurm_med_24
            high: slurm_high_24
      - rule_type: file_size
        nice_value: 0
        lower_bound: 2 GB
        upper_bound: 4 GB
        destination:
          priority:
            low: slurm_low_48
            med: slurm_med_48
            high: slurm_high_48
      - rule_type: file_size
        nice_value: 0
        lower_bound: 4 GB
        upper_bound: Infinity
        fail_message: Too much data, shoudn't run
        destination: fail
      - rule_type: arguments
        nice_value: 0
        arguments:
          careful: true
        destination:
          priority:
            low: slurm_low_48
            med: slurm_med_48
            high: slurm_high_48
    default_destination:
      priority:
        low: slurm_low_16
        med: slurm_med_16
        high: slurm_high_16

  srst2:
    rules:
      - rule_type: records
        nice_value: 0
        lower_bound: 0
        upper_bound: 100
        destination:
          priority:
            low: slurm_low_4
            med: slurm_med_4
            high: slurm_high_4
      - rule_type: records
        nice_value: 0
        lower_bound: 100
        upper_bound: 1000
        destination:
          priority:
            low: slurm_low_8
            med: slurm_med_8
            high: slurm_high_8
      - rule_type: records
        nice_value: 0
        lower_bound: 1000
        upper_bound: 10000
        destination:
          priority:
            low: slurm_low_8
            med: slurm_med_8
            high: slurm_high_8
      - rule_type: records
        nice_value: 0
        lower_bound: 1000000
        upper_bound: Infinity
        fail_message: Using the wrong tool
        destination: fail

  smalt_map:
    rules:
      - rule_type: file_size
        nice_value: 0
        lower_bound: 0
        upper_bound: 2 GB
        destination:
          priority:
            low: slurm_low_4
            med: slurm_med_4
            high: slurm_high_4
      - rule_type: file_size
        nice_value: 0
        lower_bound: 2 GB
        upper_bound: 4 GB
        destination:
          priority:
            low: slurm_low_8
            med: slurm_med_8
            high: slurm_high_8
      - rule_type: file_size
        nice_value: 0
        lower_bound: 4 GB
        upper_bound: Infinity
        destination:
          priority:
            low: slurm_low_16
            med: slurm_med_16
            high: slurm_high_16

  fastqc:
    rules:
      - rule_type: file_size
        nice_value: 0
        lower_bound: 0
        upper_bound: 400 MB
        fail_message: File size too small
        destination: fail
      - rule_type: file_size
        nice_value: 0
        lower_bound: 400 MB
        upper_bound: Infinity
        destination:
          priority:
            low: slurm_low_4
            med: slurm_med_4
            high: slurm_high_4
    default_destination:
      priority:
        low: slurm_low_16
        med: slurm_med_16
        high: slurm_high_16

default_destination:
  priority:
    low: slurm_low_default
    med: slurm_med_default
    high: slurm_high_default
users:
  user@email.com:
    priority: high
verbose: True