File: TemplateProtocol.xml

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<jellyProtocol>
    <reference>/FULL/PATH/TO__/PBJelly/data/reference/lambda.fasta</reference>  
    <outputDir>/FULL/PATH/TO__/PBJelly/lambdaExample/</outputDir>
    <cluster>
        <command notes="For single node, multi-core machines" >${CMD} ${JOBNAME} 2> ${STDERR} 1> ${STDOUT} &amp;</command>
        <command notes="For PBS/Moab">echo '${CMD}' | msub -N "${JOBNAME}" -o ${STDOUT} -e ${STDERR} -l nodes=1:ppn=8,mem=48000mb</command>
        <nJobs>1</nJobs>
    </cluster>
    <blasr>--minMatch 8 --sdpTupleSize 8 --minPctIdentity 75 --bestn 1 --nCandidates 10 --maxScore -500 --nproc 8 --noSplitSubreads</blasr>
    <input baseDir="/FULL/PATH/TO__/PBJelly/lambdaExample/data/reads/">
        <job>pacbioReads.fasta</job>
    </input>
</jellyProtocol>