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 To run jobs on an interactive queue or workstation hpcrunner.pl execute_job 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. Please see the complete documentation at HPC::Runner::Command GitBooks 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 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 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 #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 AUTHOR Jillian Rowe 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 bitbucket, 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