docker-galaxy-exome-seq/configs/job_conf.xml.miracum_sample at master · bgruening/docker-galaxy-exome-seq · GitHub

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<?xml version="1.0"?>
<job_conf>
    <plugins workers="2">
        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
            <param id="drmaa_library_path">/usr/lib/slurm-drmaa/lib/libdrmaa.so</param>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
        </plugin>
        <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner">
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_CONDOR">true</param>
        </plugin>
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
    </plugins>
    <!-- The default handler can be changed by specifying the GALAXY_HANDLERS_DEFAULT environment variable. -->
    <handlers default_from_environ="GALAXY_HANDLERS_DEFAULT" default="handlers">
        <handler id="handler0" tags="handlers"/>
        <handler id="handler1" tags="handlers"/>
        </handlers>
    <!-- The default destination can be changed by specifying the GALAXY_DESTINATIONS_DEFAULT environment variable. -->
    <destinations default_from_environ="GALAXY_DESTINATIONS_DEFAULT" default="slurm_cluster">
        <destination id="docker_dispatch" runner="dynamic">
            <!-- Allow different default destinations based on whether the tool
                 supports Docker or not. -->
            <param id="type">docker_dispatch</param>
            <param id="docker_destination_id" from_environ="GALAXY_DESTINATIONS_DOCKER_DEFAULT">slurm_cluster</param>
            <param id="default_destination_id" from_environ="GALAXY_DESTINATIONS_NO_DOCKER_DEFAULT">slurm_cluster</param>
        </destination>
        <!--destination id="singularity_dispatch" runner="dynamic">
            <param id="type">singularity_dispatch</param>
            <param id="singularity_destination_id" from_environ="GALAXY_DESTINATIONS_DOCKER_DEFAULT">slurm_cluster</param>
            <param id="default_destination_id" from_environ="GALAXY_DESTINATIONS_NO_DOCKER_DEFAULT">slurm_cluster</param>
        </destination-->
        <destination id="local_no_container" runner="local">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_LOCAL">true</param>
        </destination>
            <destination id="local_docker" runner="local">
                <env file="/galaxy_venv/bin/activate"/>
                <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_LOCAL">true</param>
                <param id="docker_enabled">true</param>
                <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">False</param>
                <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
                <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM"></param>
                <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
                <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">$defaults</param>
        </destination>
        <destination id="local_force_docker" runner="local">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_LOCAL">true</param>
            <param id="docker_enabled">true</param>
            <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">False</param>
            <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
            <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM"></param>
            <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
            <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">$defaults</param>
            <param id="docker_default_container_id" from_environ="GALAXY_DOCKER_DEFAULT_CONTAINER">busybox:ubuntu-14.04</param>
        </destination>
        <destination id="slurm_cluster" runner="slurm">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
            <param id="nativeSpecification" from_environ="NATIVE_SPEC">--ntasks=1 --share</param>
        </destination>        <!-- Docker -->
        <destination id="slurm_cluster_docker" runner="slurm">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
            <param id="docker_enabled">true</param>
            <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">False</param>
            <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
            <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM"></param>
            <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
            <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">$defaults</param>
            <param id="nativeSpecification" from_environ="NATIVE_SPEC">--ntasks=1 --share</param>
        </destination>
        <destination id="slurm_cluster_force_docker" runner="slurm">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
            <param id="docker_enabled">true</param>
            <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">False</param>
            <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
            <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM"></param>
            <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
            <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">$defaults</param>
            <param id="docker_default_container_id" from_environ="GALAXY_DOCKER_DEFAULT_CONTAINER">busybox:ubuntu-14.04</param>
            <param id="nativeSpecification" from_environ="NATIVE_SPEC">--ntasks=1 --share</param>
        </destination>
        <!-- Singularity -->
        <destination id="slurm_cluster_singularity" runner="slurm">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
            <param id="singularity_enabled">true</param>
            <param id="singularity_sudo" from_environ="GALAXY_SINGULARITY_SUDO">False</param>
            <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_SINGULARITY_VOLUMES_FROM to use. -->
            <param id="singularity_volumes_from" from_environ="GALAXY_SINGULARITY_VOLUMES_FROM"></param>
            <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
            <param id="singularity_volumes" from_environ="GALAXY_SINGULARITY_VOLUMES">$defauls</param>
            <param id="nativeSpecification" from_environ="NATIVE_SPEC">--ntasks=1 --share</param>
        </destination>
        <destination id="condor_cluster" runner="condor">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_CONDOR">true</param>
            <param id="universe" from_environ="GALAXY_CONDOR_UNIVERSE">vanilla</param>
        </destination>
        <destination id="condor_cluster_docker" runner="condor">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_CONDOR">true</param>
            <param id="docker_enabled">true</param>
            <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">False</param>
            <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
            <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM"></param>
            <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
            <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">$defaults</param>
            <param id="universe" from_environ="GALAXY_CONDOR_UNIVERSE">vanilla</param>
        </destination>
        <destination id="condor_cluster_force_docker" runner="condor">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_CONDOR">true</param>
            <param id="docker_enabled">true</param>
            <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">False</param>
            <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
            <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM"></param>
            <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
            <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">$defaults</param>
                            <param id="docker_default_container_id" from_environ="GALAXY_DOCKER_DEFAULT_CONTAINER">busybox:ubuntu-14.04</param>
           <param id="universe" from_environ="GALAXY_CONDOR_UNIVERSE">vanilla</param>
        </destination>
        <destination id="condor_docker_universe" runner="condor">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_CONDOR">true</param>
            <param id="docker_enabled">true</param>
            <param id="docker_sudo" from_environ="GALAXY_DOCKER_SUDO">False</param>
            <!-- The empty volumes from shouldn't affect Galaxy, set GALAXY_DOCKER_VOLUMES_FROM to use. -->
            <param id="docker_volumes_from" from_environ="GALAXY_DOCKER_VOLUMES_FROM"></param>
            <!-- For a stock Galaxy instance and traditional job runner $defaults will expand out as: $galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw -->
            <param id="docker_volumes" from_environ="GALAXY_DOCKER_VOLUMES">$defaults</param>
            <param id="docker_default_container_id" from_environ="GALAXY_DOCKER_DEFAULT_CONTAINER">busybox:ubuntu-14.04</param>
            <param id="universe" from_environ="GALAXY_CONDOR_UNIVERSE">docker</param>
        </destination>
        <!-- Following destinations send to basic Condor runner if no Docker image is available
             otherwise they both use the Docker image - the first submits a normal Condor job
             that will run Docker on the resulting worker node and the second uses Condor's
             native Docker universe support.
        -->
        <destination id="condor_docker_cluster_dispatch" runner="dynamic">
            <param id="type">docker_dispatch</param>
            <param id="docker_destination_id">condor_cluster</param>
            <param id="default_destination_id">condor_cluster_docker</param>
        </destination>
        <destination id="condor_docker_universe_dispatch" runner="dynamic">
            <param id="type">docker_dispatch</param>
            <param id="docker_destination_id">condor_cluster</param>
            <param id="default_destination_id">condor_docker_universe</param>
        </destination>
        <destination id="slurm-4c" runner="slurm">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
            <param id="nativeSpecification" from_environ="NATIVE_SPEC">--ntasks=1 --cpus-per-task=4</param>
        </destination>
        <destination id="slurm-8c" runner="slurm">
            <env file="/galaxy_venv/bin/activate"/>
            <param id="enabled" from_environ="GALAXY_RUNNERS_ENABLE_SLURM">true</param>
            <param id="nativeSpecification" from_environ="NATIVE_SPEC">--ntasks=1 --cpus-per-task=8</param>
        </destination>
    </destinations>
    <tools>
        <tool id="bowtie2" destination="slurm-4c"/>
        <tool id="bwa_mem" destination="slurm-8c"/>
        <tool id="lofreq_call" destination="slurm-8c"/>
        <tool id="samtools_calmd" destination="slurm-4c"/>
        <tool id="bamleftalign" destination="slurm-4c"/>
        <tool id="gemini_load" destination="slurm-4c"/>
    </tools>

    <limits>
    </limits>
</job_conf>