BioLegato

BioLegato orchestrates execution of external bioinformatics programs and pipelines on high-performance computing platforms by using PCD-described command-line invocations and configurable parameters.

Key Features:

• PCD language: Uses the PCD (Program Call Descriptor) language to specify program parameters and command-line invocations for external programs.
• External program execution: Launches and executes arbitrary command-line programs and pipelines suitable for HPC environments.
• Extensible integration via PCD files: Integrates new applications by copying and modifying PCD files without altering the BioLegato Java core.
• Object-oriented organization: Organizes applications according to discrete data types and associated methods using object-oriented principles.

Scientific Applications:

• Bioinformatics tool integration: Combines diverse analytical tools into cohesive pipelines for bioinformatics analyses.
• Cross-disciplinary workflow orchestration: Orchestrates disparate software components across scientific domains that require integrated execution on HPC systems.

Methodology:

BioLegato reads PCD files that define program parameters and command-line invocations; new tools are added by copying/modifying PCD files without changing the Java core, and applications are organized by data types and methods.