NAME

seqmule-run executes an analysis script

SYNOPSIS

    seqmule run <script_file> [options]

DESCRIPTION

This command takes a script file generated by seqmule-pipelien and executes it from the first step among all unfinished steps.

OPTIONS

    -n <INT>                run from step INT
    --sge <TEXT>            run each command via Sun Grid Engine. A template with XCPUX keyword is expected.
    -h,--help               help

EXAMPLES

    #continue run from last executed step
    seqmule run your_analysis.script

    #run from a certain step
    seqmule run -n 10 your_analysis.script

    #run via Sun Grid Engine (a job scheduling system)
    seqmule run -sge "qsub -V -cwd -pe smp XCPUX" your_analysis.script

DETAILS

  • --sge

    To run commands via Sun Grid Engine, SGE must be installed first. -e, -o will be added automatically. "-S /bin/bash" is added automatically. Do NOT specify -e,-o or -S in the qsub template.