job_conf.xml

job_conf.xml

<?xml version="1.0"?>

-<job_conf>


-<plugins workers="4">

<plugin load="galaxy.jobs.runners.slurm:SlurmJobRunner" type="runner" id="slurm"/>

<plugin load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner" type="runner" id="pulsar_rest"/>

<plugin workers="10" load="galaxy.jobs.runners.local:LocalJobRunner" type="runner" id="local"/>

</plugins>


-<handlers default="main">


-<handler id="main" tags="handlers">

<plugin id="slurm"/>

</handler>

</handlers>


-<destinations default="slurm_cluster">

<destination id="slurm_cluster" runner="slurm"/>


-<destination id="slurm_cluster_cpu4" runner="slurm">

<param id="nativeSpecification">--nodes=1 --ntasks=4</param>

</destination>


-<destination id="slurm_cluster_cpu15" runner="slurm">

<param id="nativeSpecification">--nodes=1 --ntasks=15</param>

</destination>


-<destination id="slurm_cluster_cpu30" runner="slurm">

<param id="nativeSpecification">--nodes=1 --ntasks=30</param>

</destination>


-<destination id="pulsar_server" runner="pulsar_rest">

<param id="url">http://pulsar_server_ip:pulsar_server_port/</param>

</destination>

<destination id="local_runner" runner="local"/>

</destinations>


-<tools>

<!-- <tool id="upload1" destination="local_runner" /> -->


<!-- <tool id="random_lines1" destination="pulsar_server" /> -->


<tool id="bowtie" destination="slurm_cluster_cpu4"/>

<tool id="bowtie2" destination="slurm_cluster_cpu15"/>

<tool id="sailfish" destination="slurm_cluster_cpu4"/>

<tool id="cuffmerge" destination="slurm_cluster_cpu4"/>

<tool id="cufflinks" destination="slurm_cluster_cpu4"/>

<tool id="currnorm" destination="slurm_cluster_cpu4"/>

<tool id="bwa" destination="slurm_cluster_cpu15"/>

<tool id="tophat_fusion" destination="slurm_cluster_cpu4"/>

<tool id="cuffquant" destination="slurm_cluster_cpu4"/>

<tool id="cuffdiff" destination="slurm_cluster_cpu4"/>

<tool id="bowtie2" destination="slurm_cluster_cpu15"/>

<tool id="trimmomatic" destination="slurm_cluster_cpu4"/>

<tool id="hisat2" destination="slurm_cluster_cpu4"/>

<tool id="pear" destination="slurm_cluster_cpu4"/>

<tool id="diamond" destination="slurm_cluster_cpu4"/>

<tool id="spades" destination="slurm_cluster_cpu4"/>

<tool id="kraken" destination="slurm_cluster_cpu15"/>

<tool id="hydra" destination="slurm_cluster_cpu15"/>

<tool id="freebayes" destination="slurm_cluster_cpu30"/>

<tool id="snippy" destination="slurm_cluster_cpu30"/>

</tools>

</job_conf>