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README.md

project

When submitting jobs we will prepend the jobname with the project name

NAME

HPC::Runner::Command - Create composable bioinformatics hpc analyses.

SYNOPSIS

To create a new project

hpcrunner.pl new MyNewProject

To submit jobs to a cluster

hpcrunner.pl submit_jobs --infile my_submission.sh

To run jobs on an interactive queue or workstation

hpcrunner.pl single_node --infile my_submission.sh

DESCRIPTION

HPC::Runner::Command is a set of libraries for scaffolding data analysis projects, submitting and executing jobs on an HPC cluster or workstation, and obsessively logging results.

Get help by heading on over to github and raising an issue. [GitHub ](https://metacpan.org/pod/ https:#github.com-biosails-HPC-Runner-Command-issues).

Please see the complete documentation at [HPC::Runner::Command GitBooks ](https://metacpan.org/pod/ https:#biosails.gitbooks.io-hpc-runner-command-docs-content).

Quick Start - Create a New Project

You can create a new project, with a sane directory structure by using

    hpcrunner.pl new MyNewProject

Quick Start - Submit Workflows

Simple Example

Our simplest example is a single job type with no dependencies - each task is independent of all other tasks.

Workflow file

    #preprocess.sh

    echo "preprocess" && sleep 10;
    echo "preprocess" && sleep 10;
    echo "preprocess" && sleep 10;

Submit to the scheduler

    hpcrunner.pl submit_jobs --infile preprocess.sh

Look at results!

    tree hpc-runner

Audit your results

hpcrunner.pl stats -h
hpcrunner.pl stats

Job Type Dependencency Declaration

Most of the time we have jobs that depend upon other jobs.

Workflow file

    #blastx.sh

    #HPC jobname=unzip
    unzip Sample1.zip
    unzip Sample2.zip
    unzip Sample3.zip

    #HPC jobname=blastx
    #HPC deps=unzip
    blastx --db env_nr --sample Sample1.fasta
    blastx --db env_nr --sample Sample2.fasta
    blastx --db env_nr --sample Sample3.fasta

Submit to the scheduler

    hpcrunner.pl submit_jobs --infile preprocess.sh

Look at results!

    tree hpc-runner

Task Dependencency Declaration

Within a job type we can declare dependencies on particular tasks.

Workflow file

    #blastx.sh

    #HPC jobname=unzip
    #TASK tags=Sample1
    unzip Sample1.zip
    #TASK tags=Sample2
    unzip Sample2.zip
    #TASK tags=Sample3
    unzip Sample3.zip

    #HPC jobname=blastx
    #HPC deps=unzip
    #TASK tags=Sample1
    blastx --db env_nr --sample Sample1.fasta
    #TASK tags=Sample2
    blastx --db env_nr --sample Sample2.fasta
    #TASK tags=Sample3
    blastx --db env_nr --sample Sample3.fasta

Submit to the scheduler

    hpcrunner.pl submit_jobs --infile preprocess.sh

Look at results!

    tree hpc-runner

Audit your results

hpcrunner.pl stats -h
hpcrunner.pl stats

Declare Scheduler Variables

Each scheduler has its own set of variables. HPC::Runner::Command has a set of generalized variables for declaring types across templates. For more information please see Job Scheduler Comparison

Additionally, for workflows with a large number of tasks, please see Considerations for Workflows with a Large Number of Tasks for information on how to group tasks together.

Workflow file

      #blastx.sh

      #HPC jobname=unzip
      #HPC cpus_per_task=1
      #HPC partition=serial
      #HPC commands_per_node=1
#HPC mem=4GB
      #TASK tags=Sample1
      unzip Sample1.zip
      #TASK tags=Sample2
      unzip Sample2.zip
      #TASK tags=Sample3
      unzip Sample3.zip

      #HPC jobname=blastx
      #HPC cpus_per_task=6
      #HPC deps=unzip
      #TASK tags=Sample1
      blastx --threads 6 --db env_nr --sample Sample1.fasta
      #TASK tags=Sample2
      blastx --threads 6 --db env_nr --sample Sample2.fasta
      #TASK tags=Sample3
      blastx --threads 6 --db env_nr --sample Sample3.fasta

Submit to the scheduler

    hpcrunner.pl submit_jobs --infile preprocess.sh

Look at results!

    tree hpc-runner

Audit your results

hpcrunner.pl stats -h
hpcrunner.pl stats

AUTHOR

Jillian Rowe jillian.e.rowe@gmail.com

Previous Release

This software was previously released under HPC::Runner. HPC::Runner::Command is a complete rewrite of the existing library. While it is meant to have much of the same functionality, it is not backwords compatible.

Acknowledgements

As of Version 2.41:

This modules continuing development is supported by NYU Abu Dhabi in the Center for Genomics and Systems Biology. With approval from NYUAD, this information was generalized and put on github, for which the authors would like to express their gratitude.

Before Version 2.41

This module was originally developed at and for Weill Cornell Medical College in Qatar within ITS Advanced Computing Team. With approval from WCMC-Q, this information was generalized and put on github, for which the authors would like to express their gratitude.

COPYRIGHT

Copyright 2016- Jillian Rowe

LICENSE

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

SEE ALSO

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