job_conf.xml.cloud

<?xml version="1.0"?>
<job_conf>
    <plugins workers="4">
        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
            <param id="drmaa_library_path">/mnt/galaxy/slurm-drmaa/lib/libdrmaa.so</param>
        </plugin>
        <plugin id="pulsar_rest" type="runner" load="galaxy.jobs.runners.pulsar:PulsarRESTJobRunner" />
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4" />
    </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="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_cpu4"/>
        <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_cpu4"/>
        <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_cpu4"/>
        <tool id="tophat2" destination="slurm_cluster_cpu4"/>
        <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="fastqc" destination="slurm_cluster_cpu4"/>
        <tool id="stringtie" destination="slurm_cluster_cpu4"/>
        <tool id="tsne" destination="slurm_cluster_cpu4"/>
        <tool id="heatmap2" destination="slurm_cluster_cpu4"/>
        <tool id="flagstat" destination="slurm_cluster_cpu4"/>
        <tool id="deseq2" destination="slurm_cluster_cpu4"/>
        <tool id="featurecounts" destination="slurm_cluster_cpu4"/>
</tools>
</job_conf>