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job_conf.yml
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---
# This is a file of variables that will be processed in job_conf.yml.j2
# This is needed, because it contains other variables
galaxy_jobconf:
plugin_workers: 8
handlers:
count: "{{ galaxy_systemd_handlers }}"
assign_with: db-skip-locked
max_grab: 16
ready_window_size: 32
plugins:
#- id: drmaa
#load: galaxy.jobs.runners.drmaa:DRMAAJobRunner
#workers: 3
- id: condor
load: galaxy.jobs.runners.condor:CondorJobRunner
- id: local
load: galaxy.jobs.runners.local:LocalJobRunner
- id: pulsar_embedded
load: galaxy.jobs.runners.pulsar:PulsarEmbeddedJobRunner
pulsar_config: "{{ galaxy_config_dir }}/pulsar_app.yml"
- id: pulsar_eu_it01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_it01:{{ rabbitmq_password_galaxy_it01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_it01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_mira_runner
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_mira_pulsar:{{ rabbitmq_password_galaxy_mira_pulsar }}@mq.galaxyproject.eu:5671//pulsar/galaxy_mira_pulsar?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_sanjay_runner
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_sanjay_pulsar:{{ rabbitmq_password_galaxy_sanjay_pulsar }}@mq.galaxyproject.eu:5671//pulsar/galaxy_sanjay_pulsar?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_sk01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_sk01:{{ rabbitmq_password_galaxy_sk01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_sk01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_it02
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_it02:{{ rabbitmq_password_galaxy_it02 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_it02?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_it03
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_it03:{{ rabbitmq_password_galaxy_it03 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_it03?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_pt01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_pt01:{{ rabbitmq_password_galaxy_pt01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_pt01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_be01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_be01:{{ rabbitmq_password_galaxy_be01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_be01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_uk01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_uk01:{{ rabbitmq_password_galaxy_uk01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_uk01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_fr01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_fr01:{{ rabbitmq_password_galaxy_fr01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_fr01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_fi01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_fi01:{{ rabbitmq_password_galaxy_fi01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_fi01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_no01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_no01:{{ rabbitmq_password_galaxy_no01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_no01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_es01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_es01:{{ rabbitmq_password_galaxy_es01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_es01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_cz01
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_cz01:{{ rabbitmq_password_galaxy_cz01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_cz01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: production
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
- id: pulsar_eu_cz02
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_cz01:{{ rabbitmq_password_galaxy_cz01 }}@mq.galaxyproject.eu:5671//pulsar/galaxy_cz01?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: gpu
amqp_acknowledge: "true"
amqp_ack_republish_time: 300
amqp_consumer_timeout: 2.0
amqp_publish_retry: "true"
amqp_publish_retry_max_retries: 60
default_destination: tpv_dispatcher
destinations:
- id: local
runner: local
- id: tpv_dispatcher
runner: dynamic
type: python
function: map_tool_to_destination
rules_module: tpv.rules
tpv_config_files:
- "{{ galaxy_config_dir }}/total_perspective_vortex/tool_defaults.yml"
- "https://raw.githubusercontent.com/galaxyproject/tpv-shared-database/main/tools.yml"
- "{{ galaxy_config_dir }}/total_perspective_vortex/destinations.yml"
- "{{ galaxy_config_dir }}/total_perspective_vortex/tools.yml"
- "{{ galaxy_config_dir }}/total_perspective_vortex/interactive_tools.yml"
- "{{ galaxy_config_dir }}/total_perspective_vortex/users.yml"
- "{{ galaxy_config_dir }}/total_perspective_vortex/roles.yml"
tools:
# TODO(hxr): implement validation that checks that every destination
# used here is defined above.
- id: keras_train_and_eval
resources: usegpu
- id: gmx_sim
resources: usegpu
resources:
- id: usegpu
names: [gpu]
limits:
- type: "destination_user_concurrent_jobs"
id: "condor_upload"
value: "10"
- type: "walltime"
value: "'148:00:00'"
# Limited time for Interactive tools
- type: "destination_user_concurrent_jobs"
value: "4"
id: "interactive_pulsar"
- type: "destination_user_concurrent_jobs"
value: "4"
id: "interactive_pulsar_hi_mem"
- type: "output_size"
value: "'300GB'"
- type: "registered_user_concurrent_jobs"
value: "30"
- type: "anonymous_user_concurrent_jobs"
value: "3"
- type: "destination_user_concurrent_jobs"
id: "sh_fdid_condor_docker_ie"
value: "3"
- type: "destination_user_concurrent_jobs"
id: "sh_fdid_condor_docker_ie_interactive"
value: "3"
- type: "destination_user_concurrent_jobs"
id: "sh_fdid_condor_intensive_jobs"
value: "10"