kronos: A workflow assembler for cancer genome analytics and informatics

kronos is a software tool for automating reproducible, auditable and distributable bioinformatics workflow development. Kronos obviates explicit coding for workflow development to a great extent by compiling a text configuration file into an executable Python scripts. Each resulting workflow includes a run manager to automatically execute the workflow locally, on a cluster or in the cloud, to parallelize tasks, and to log all runtime events. The workflows are highly modular and configurable by construction, facilitating flexible and extensible workflows which can be modified easily through configuration file editing.

kronos is a free and open source Python package under the MIT license and is shipped with both a Docker image and an Amazon machine image.

Table of Contents

• Getting started
  • Download
  • Dependencies
  • Install
• Package
  • kronos features
  • kronos commands
    • make_component
    • make_config
    • update_config
    • init
    • run
• Configuration file
  • Pipeline_info section
  • General section
  • Shared section
    • Connections
      • IO connection
  • Samples section
  • Task section
    • Reserved subsection
    • Run subsection
      • use_cluster
      • memory
      • num_cpus
      • forced_dependencies
      • add_breakpoint
      • env_var
      • boilerplate
      • parallel_run
      • parallel_params
      • interval_file
    • Component subsection
  • More on the configuration file
    • configuration file flags
    • configuration file keywords
    • configuration file reserved keywords
    • Output directory customization
• Components
  • Develop a component
    • Component_main
      • focus method
      • make_cmd method
      • ComponentAbstract class
    • Component_params
    • Component_reqs
    • Component_ui
    • component_seed
    • Examples
  • Components repository
• Pipelines
  • Create a new pipeline
    • Examples
    • Pipelines repository
  • Launch a pipeline
    • 1. Run the pipeline using run command
      • Input options of run command
      • On --qsub-options option
      • Initialize using run command
      • Run the tasks locally, on a cluster or in the cloud
    • 2. Run the pipeline using init command and the resulting pipeline script
      • Samples file
      • Setup file
      • Run the pipeline script generated by init command
      • What is the components directory?
    • Results generated by a pipeline
      • What is the working directory?
      • What is the run ID?
      • What is the structure of the results directory generated by a pipeline?
      • How can I relaunch a pipeline?
• Guides
  • Guide for Deploying Kronos to the Cloud
    • Setup StarCluster
      • Installing StarCluster
      • Creating an EBS Volume
      • Launching Your Cloud Cluster
    • Setup Kronos
• License
• Contacts
  • Questions and feedback

Author

13. Jafar Taghiyar jafar.taghiyar@gmail.com

Date last updated

2016-03-18