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test.yml
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---
- hosts: localhost
vars:
galaxy_handler_count: 4
galaxy_instance_codename: main
galaxy_jobconf:
plugin_workers: 4
handlers:
count: "{{ galaxy_handler_count }}"
assign_with: db-skip-locked
plugins:
- id: drmaa
load: galaxy.jobs.runners.drmaa:DRMAAJobRunner
workers: 3
# These live on the pythonpath
- id: dynamic
params:
rules_module: 'usegalaxy'
- id: condor
load: galaxy.jobs.runners.condor:CondorJobRunner
- id: local
load: galaxy.jobs.runners.local:LocalJobRunner
- id: pulsar_eu_cz
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_cz:@proxy.galaxyproject.eu:5671//pulsar/galaxy_cz?ssl=1"
galaxy_url: "https://usegalaxy.eu"
manager: _default_
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_test
load: galaxy.jobs.runners.pulsar:PulsarMQJobRunner
params:
amqp_url: "pyamqp://galaxy_test:@proxy.galaxyproject.eu:5671//pulsar/galaxy_test?ssl=1"
galaxy_url: https://usegalaxy.eu
manager: _default_
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: gateway_1x
destinations:
- id: local
runner: local
- id: condor
runner: condor
params:
tmp_dir: "True"
# Gateways
- id: gateway_1x
runner: dynamic
params:
type: python
function: gateway_1x
- id: gateway_1_5x
runner: dynamic
params:
type: python
function: gateway_1_5x
- id: gateway_2x
runner: dynamic
params:
type: python
function: gateway_2x
# Pulsar MQs
- id: remote_cluster_mq_cz
runner: pulsar_eu_cz
params:
jobs_directory: /storage/brno11-elixir/home/galaxyeu/galaxy-staging/
- id: remote_cluster_mq_test
runner: pulsar_eu_test
params:
jobs_directory: /data/share
- id: condor_singularity
runner: condor
params:
singularity_enabled: 'true'
singularity_volumes: '$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro'
singularity_default_container_id: '/data/0/cvmfs/singularity/ubuntu:18.04'
- id: condor_singularity2
runner: condor
params:
singularity_enabled: 'true'
singularity_volumes: '$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro'
singularity_default_container_id: '/data/0/cvmfs/singularity/ubuntu:18.04'
raw: |
<param id="container">
<container type="singularity" shell="/bin/sh" resolve_dependencies="true">/data/0/cvmfs/singularity/ubuntu:18.04</container>
</param>
- id: condor_singularity_with_conda
runner: condor
params:
singularity_enabled: 'true'
raw: |
<param id="container">
<container type="singularity" shell="/bin/bash" resolve_dependencies="true">/data/0/cvmfs/singularity/python:2.7.12--1</container>
</param>
- id: condor_docker
runner: condor
params:
docker_enabled: 'true'
docker_volumes: '$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$job_directory:rw,/data/db/:ro,/data/dnb01/galaxy_db/:ro,/data/dnb02/galaxy_db/:ro'
docker_default_container_id: 'ubuntu:18.04'
docker_auto_rm: 'true'
docker_sudo: 'false'
# TODO(hxr): check functionality
- id: 24cores_15G_BLAST
runner: dynamic
params:
type: python
function: blast_destinations
- id: wig_to_bigWig
runner: dynamic
params:
type: python
function: wig_to_bigwig
- id: dexseq_dynamic
runner: dynamic
params:
type: python
function: dexseq
tools:
# TODO(hxr): implement validation that checks that every destination
# used here is defined above.
- id: upload1
destination: gateway_1x
- id: wig_to_bigWig
destination: wig_to_bigWig
- id: dexseq
destination: dexseq_dynamic
- id: ncbi_blastn_wrapper
destination: 24cores_15G_BLAST
- id: ncbi_blastx_wrapper
destination: 24cores_15G_BLAST
- id: ncbi_tblastn_wrapper
destination: 24cores_15G_BLAST
- id: ncbi_tblastx_wrapper
destination: 24cores_15G_BLAST
- id: ncbi_blastp_wrapper
destination: 24cores_15G_BLAST
- id: ncbi_rpsblast_wrapper
destination: 24cores_15G_BLAST
limits:
walltime: '148:00:00'
output_size: '300GB'
registered_user_concurrent_jobs: '30'
anonymous_user_concurrent_jobs: '10'
roles:
- test