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qianyuanzhuqianyuanzhu
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add job runnner select field
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-11
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+107
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‎form.yml

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Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@ form:
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- bc_num_hours
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- node_type
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- num_cores
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- job_runner
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- bc_email_on_started
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attributes:
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num_cores:
@@ -37,3 +38,17 @@ attributes:
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- [ "any", "any" ]
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- [ "hugemem", "hugemem" ]
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- [ "debug", "debug" ]
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job_runner:
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widget: select
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label: "Galaxy tool runner"
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help: |
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- **local** - When running tools locally, they are child processes of the Galaxy server.
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The maximum number of concurrent jobs is the number of cores.
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When session ends, you lose contact with those jobs still running,
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and they must be restarted.
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- **cluster** - When running tools in a cluster, they are separate processes from the Galaxy server.
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They are jobs submitted to Owens Cluster as configured above and there is no maximum number of concurrent jobs.
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When session ends, the jobs will continue to run and finish.
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options:
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- [ "local", "local"]
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- [ "cluster", "pbs" ]

‎install-galaxy.sh

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@@ -7,6 +7,41 @@ fi
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cd galaxy
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git checkout release_19.09
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# Add job rules
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(
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umask 077
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cat > "./lib/galaxy/jobs/rules/destinations.py" << EOL
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import logging
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from galaxy.jobs.mapper import JobMappingException
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from galaxy.jobs import JobDestination
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log = logging.getLogger(__name__)
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FAILURE_MESSAGE = 'This tool could not be run because of a misconfiguration in the Galaxy job running system, please report this error'
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def dynamic_cores_time(app, tool, job, user_email, resource_params):
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# handle job resource parameters
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if not resource_params.get("cores") and not resource_params.get("time"):
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default_destination_id = app.job_config.get_destination(None)
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log.warning('(%s) has no input parameter cores or time. Run with default runner: %s' % (job.id, default_destination_id.runner))
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return default_destination_id
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try:
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cores = resource_params.get("cores")
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time = resource_params.get("time")
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resource_list = 'walltime=%s:00:00,nodes=1:ppn=%s' % (time, cores)
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except:
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default_destination_id = app.job_config.get_destination(None)
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log.warning('(%s) failed to run with customized configuration. Run with default runner: %s' % (job.id, default_destination_id.runner))
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return default_destination_id
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log.info('returning pbs runner with configuration %s', resource_list)
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return JobDestination(runner="pbs", params={"Resource_List": resource_list})
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EOL
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)
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# Install dependencies
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# Retrieved from line 1-54 in https://github.com/galaxyproject/galaxy/blob/release_19.09/run.sh
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. ./scripts/common_startup_functions.sh

‎manifest.yml

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Original file line numberDiff line numberDiff line change
@@ -6,5 +6,5 @@ role: batch_connect
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description: |
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This app will launch [Galaxy 19.09] on the [Owens cluster].
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9-
[Galaxy]: https://galaxyproject.org/
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[Galaxy 19.09]: https://galaxyproject.org/
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[Owens cluster]: https://www.osc.edu/resources/technical_support/supercomputers/owens

‎template/before.sh.erb

Lines changed: 56 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -11,6 +11,8 @@ MOUNT="/node/${HOSTNAME}/8080=galaxy.webapps.galaxy.buildapp:uwsgi_app()"
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DATAROOT=${HOME}/.galaxy
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EMAIL="${USER}@osc.edu"
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export JOB_CONFIG_FILE_PATH="${PWD}/job_conf.xml"
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export JOB_RESOURCE_PARAMS_CONF_FILE_PATH="${PWD}/job_resource_params_conf.xml"
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export WORKFLOW_RESOURCE_PARAMS_CONF_FILE_PATH="${PWD}/workflow_resource_params_conf.xml"
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echo "GALAXY location: '${GALAXY_PATH}'"
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echo "Data location: '${DATAROOT}'"
@@ -33,27 +35,67 @@ cat > "${JOB_CONFIG_FILE_PATH}" << EOL
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<?xml version="1.0"?>
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<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
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<job_conf>
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<resources>
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<group id="basic">cores,time</group>
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</resources>
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<tools>
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<tool id="bed2gff1" destination="dynamic_cores_time" resources="basic"/>
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</tools>
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<plugins>
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<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
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<plugin id="pbs" type="runner" load="galaxy.jobs.runners.pbs:PBSJobRunner"/>
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<plugin id="dynamic" type="runner">
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<param id="rules_module">galaxy.jobs.rules</param>
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</plugin>
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</plugins>
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<destinations default="pbs_default">
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<destination id="pbs_default" runner="pbs">
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<param id="Resource_List">walltime=5:00:00,nodes=1:ppn=<%= ppn %></param>
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<param id="-p">128</param>
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<destinations default="<%= context.job_runner %>">
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<destination id="dynamic_cores_time" runner="dynamic">
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<param id="type">python</param>
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<param id="function">dynamic_cores_time</param>
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</destination>
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<destination id="other_cluster" runner="pbs">
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<param id="destination">@other.cluster</param>
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<destination id="pbs" runner="pbs">
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<param id="Resource_List">walltime=5:00:00,nodes=1:ppn=<%= ppn %></param>
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</destination>
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<destination id="long_jobs" runner="pbs">
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<param id="Resource_List">walltime=5:00:00,nodes=1:ppn=1</param>
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<param id="-p">128</param>
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<param id="Output_Path"></param>
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<destination id="local" runner="local">
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<param id="local_slots"><%= ppn %></param>
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</destination>
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</destinations>
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</job_conf>
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EOL
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)
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# Generate Galaxy job resource parameter configuration file
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(
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umask 077
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cat > "${JOB_RESOURCE_PARAMS_CONF_FILE_PATH}" << EOL
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<parameters>
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<param label="Cores" name="cores" type="integer" min="1" max="28" value="1" help="Number of processing cores, 'ppn' value (1-28). Leave blank to use default value." />
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<param label="Walltime" name="time" type="integer" size="3" min="1" max="24" value="1" help="Maximum job time in hours, 'walltime' value (1-24). Leave blank to use default value." />
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</parameters>
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EOL
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)
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# Generate Galaxy workflow resource parameter configuration file
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(
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umask 077
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cat > "${WORKFLOW_RESOURCE_PARAMS_CONF_FILE_PATH}" << EOL
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<parameters>
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<param label="Processors" name="processors" type="integer" min="1" max="28" value="" help="Number of processing cores, 'ppn' value (1-28). Leave blank to use default value." />
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<param label="Memory" name="memory" type="integer" min="1" max="256" value="" help="Memory size in gigabytes, 'pmem' value (1-256). Leave blank to use default value." />
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<param label="Time" name="time" type="integer" min="1" max="744" value="" help="Maximum job time in hours, 'walltime' value (1-744). Leave blank to use default value." />
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<param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value." />
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<param label="Workflow Job Priority" name="priority" type="select" value="med" help="What priority should the jobs in this workflow run at? (Overrides any declared job priority)">
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<option value="low" label="Low"/>
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<option value="med" label="Medium"/>
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<option value="high" label="High"/>
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<option value="ultra" label="Ultra"/>
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<option value="plus_ultra" label="Plus Ultra"/>
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</param>
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</parameters>
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EOL
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)
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# Generate Galaxy configuration file
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(
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umask 077
@@ -82,5 +124,9 @@ galaxy:
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data_dir: ${DATAROOT}
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single_user: ${EMAIL}
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tool_dependency_dir: ${GALAXY_PATH}/database/dependencies
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job_resource_params_file: ${JOB_RESOURCE_PARAMS_CONF_FILE_PATH}
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workflow_resource_params_file: ${WORKFLOW_RESOURCE_PARAMS_CONF_FILE_PATH}
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admin_users: ${EMAIL}
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job_config_file: ${JOB_CONFIG_FILE_PATH}
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EOL
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)

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