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What is BioLockJ#

BioLockJ optimizes your bioinformatics pipeline and metagenomics analysis.

• Modular design logically partitions analysis and expedites failure recovery
• Automated script generation eliminates syntax errors and ensures uniform execution
• Standardized OTU abundance tables facilitate analysis across datasets
• Batch scripts take advantage of parallelization on the cluster job queue
• configuration file consolidates project details into a principal reference document (and can reproduce analysis)
• BioModule interface provides a flexible mechanism for adding new functionality

BioLockJ User Guide:#

• Getting Started
• Commands
• Pipeline Componenets
  • the config file
    • Properties
    • Modules
  • the metadata
  • input files
  • Dependencies
• Features
  • Check Dependencies before pipeline start
  • Failure Recovery
  • Validation
  • Supported Environments
  • Expand BioLockJ by Building Modules
  • BioLockJ API
• Examples and Templates
  • Example Pipeline
• FAQ & Troubleshooting

Links for Developers#

BioLockJ Developers Guide

Repository of functional tests
https://github.com/BioLockJ-Dev-Team/sheepdog_testing_suite

The user guide for our latest stable version
https://biolockj-dev-team.github.io/BioLockJ/

The user guide for the current development version, and previous stable versions
https://biolockj.readthedocs.io/en/latest/

Guidelines for new modules
Building Modules

Citing BioLockJ#

If you use BioLockJ in your research, you should cite BioLockJ itself AND the tools that make up the pipeline. The majority of BioLockJ modules are wrappers for independent tools. See the summary of your pipeline for citation information from the modules in your pipeline. This information is also available in the modules' documentation.

To cite BioLockJ itself, please cite the public project git repository (https://github.com/BioLockJ-Dev-Team/BioLockJ) and author Mike Sioda.