2 handlers, a few jobs that reserve more cores.
<?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" workers="4"/>
<plugin id="gridengine" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner">
<!-- Override the $DRMAA_LIBRARY_PATH environment variable -->
<param id="drmaa_library_path">/opt/gridengine/lib/linux-x64/libdrmaa.so</param>
</plugin>
</plugins>
<handlers default="handlers">
<handler id="handler0" tags='handlers'>
<plugin id="gridengine"/>
</handler>
<handler id="handler1" tags='handlers'>
<plugin id="gridengine"/>
</handler>
</handlers>
<destinations default="gridengine">
<destination id="local" runner="local"/>
<destination id="gridengine" runner="gridengine" tags="rockscluster">
<param id="embed_metadata_in_job">True</param>
<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>
</destination>
<destination id="gridengine_8" runner="gridengine" tags="rockscluster,8cores">
<param id="embed_metadata_in_job">True</param>
<param id="nativeSpecification">-pe smp 8</param>
<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>
</destination>
<destination id="gridengine_16" runner="gridengine" tags="rockscluster,16cores">
<param id="embed_metadata_in_job">True</param>
<param id="nativeSpecification">-pe smp 16</param>
<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>
</destination>
<destination id="gridengine_16_long" runner="gridengine" tags="rockscluster,16cores,longrun">
<param id="embed_metadata_in_job">True</param>
<param id="nativeSpecification">-pe smp 16 -P longrun</param>
<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>
</destination>
<destination id="gridengine_32_long" runner="gridengine" tags="rockscluster,32cores,longrun">
<param id="embed_metadata_in_job">True</param>
<param id="nativeSpecification">-pe smp 32 -P longrun</param>
<env exec="source /mnt/galaxy/data/galaxy/cluster_env/bin/activate"/>
</destination>
</destinations>
<tools>
<tool id="bowtie2" destination="8cores"/>
<tool id="bismark_bowtie2" destination="8cores"/>
<tool id="freebayes" destination="8cores"/>
<tool id="tophat2" destination="8cores"/>
<tool id="hisat" destination="8cores"/>
<tool id="hisat2" destination="8cores"/>
<tool id="trinityrnaseq" destination="longrun"/>
<tool id="cufflinks" destination="8cores"/>
<tool id="stringtie" destination="16cores"/>
<tool id="mira_4_0_de_novo" destination="8cores"/>
</tools>
<limits>
<limit type="destination_total_concurrent_jobs" id="local">8</limit>
</limits>
</job_conf>