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job_conf.xml
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<?xml version="1.0"?>
<job_conf>
<plugins workers="4">
<!--"workers" is the number of threads for the runner's work queue.-->
<!--The default from <plugins> is used if not defined for a </plugin>.-->
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
<!--<param id="drmaa_library_path">/opt/condor/lib/libdrmaa.so</param>-->
<param id="drmaa_library_path">drmaa/drmaa/libdrmaa.so</param>
<!-- Different DRMs handle successfully completed jobs differently,
these options can be changed to handle such differences and
are explained in detail on the Galaxy wiki. Defaults are shown -->
<!--<param id="invalidjobexception_state">ok</param>-->
<!--<param id="invalidjobexception_retries">0</param>-->
<!--<param id="internalexception_state">ok</param>-->
<!--<param id="internalexception_retries">0</param>-->
</plugin>
</plugins>
<handlers default="main">
<handler id="main" tags="handlers"/>
<!-- Additional job handlers - the id should match the name of a
[server:id] in universe_wsgi.ini.
-->
</handlers>
<destinations default="docker_condor_16C_16G">
<!-- Destinations define details about remote resources and how jobs
should be executed on those remote resources.
-->
<destination id="local" runner="local" metrics="off"/>
<destination id="docker_condor_16C_16G" runner="drmaa">
<param id="nativeSpecification">getenv=True\nrequest_cpus=16\nrequest_memory=16 GB</param>
</destination>
<destination id="condor_galaxy" runner="drmaa" metrics="off">
<param id="nativeSpecification">getenv=True\nrequest_cpus=2\nrequest_memory=8 GB\nrequirements=(machine=="exanode-0-23.local")</param>
</destination>
<destination id="condor_2C_2G" runner="drmaa">
<param id="nativeSpecification">getenv=True\nrequest_cpus=2\nrequest_memory=2 GB</param>
</destination>
<destination id="condor_1C_100M" runner="drmaa">
<param id="nativeSpecification">getenv=True\nrequest_cpus=1\nrequest_memory=100 MB</param>
</destination>
<destination id="docker_condor_16C_16G" runner="drmaa">
<param id="docker_enabled">true</param>
<param id="docker_volumes">$defaults</param>
<param id="nativeSpecification">getenv=True\nrequest_cpus=16\nrequest_memory=16 GB</param>
</destination>
<destination id="condor_1C_100M_ADAM" runner="drmaa">
<param id="docker_enabled">true</param>
<param id="docker_volumes">$defaults</param>
<!--param id="nativeSpecification">getenv=True\nrequest_cpus=1\nrequest_memory=100 MB\njob_type=adam\nmachine_name=SPARK\nrequirements=(machine=="v10.cluster5.ccc.com" || machine=="v12.cluster5.ccc.com")</param-->
<param id="nativeSpecification">getenv=True\nrequest_cpus=1\nrequest_memory=100 MB\njob_type=adam\nmachine_name=SPARK\nrequirements=(TARGET.SPARK_COMPUTE_NODE =?= True)</param>
</destination>
</destinations>
<tools>
<!-- Tools can be configured to use specific destinations or handlers,
identified by either the "id" or "tags" attribute. If assigned to
a tag, a handler or destination that matches that tag will be
chosen at random.
<tool id="cbioportal_create_files" destination="condor_galaxy"/>
<tool id="cbioportal_importer_tool" destination="condor_galaxy"/>
<tool id="cbioportal_get_database_info" destination="condor_galaxy"/>
<tool id="product_map" destination="condor_2C_2G"/>
<tool id="sum_reduce" destination="condor_2C_2G"/>
<tool id="getAnnotation" destination="condor_2C_2G"/>
<tool id="upload1" destination="condor_1C_100M"/>
-->
<tool id="transform_bam_to_adam" destination="condor_1C_100M_ADAM"/>
<tool id="transform_sort" destination="condor_1C_100M_ADAM"/>
<tool id="transform_mark_duplicates" destination="condor_1C_100M_ADAM"/>
<tool id="convert_vcf_to_adam" destination="condor_1C_100M_ADAM"/>
<tool id="transform_recalibrate_base_qualities" destination="condor_1C_100M_ADAM"/>
<tool id="transform_realign_indels" destination="condor_1C_100M_ADAM"/>
</tools>
<limits>
<!-- Certain limits can be defined. -->
<limit type="registered_user_concurrent_jobs">100</limit>
<limit type="unregistered_user_concurrent_jobs">2</limit>
<limit type="job_walltime">24:00:00</limit>
<!--<limit type="concurrent_jobs" id="local">1</limit>-->
<!--<limit type="concurrent_jobs" tag="mycluster">2</limit>-->
<!--<limit type="concurrent_jobs" tag="longjobs">1</limit>-->
</limits>
</job_conf>