SCARAB

Getting started

  • Installation
    • 1. Released Mamba/Conda package
    • 2. Docker
    • 3. Apptainer
    • 4. GitHub source installation
    • Installation verification
  • Your first recruitment run
    • Prepare three inputs
    • Run
    • Review
  • Tiny installation and workflow demo
    • Get the bundled inputs
    • Mamba package or source installation
    • Docker
    • Apptainer
    • What success means
    • Provenance
  • Input files
    • Read lists
    • Trusted references
    • Contig tiling

Workflow and interpretation

  • SCARAB workflow
    • Conceptual overview
    • Software architecture
    • Detailed data flow
    • What the workflow reconstructs
    • Follow the evidence through recruitment
    • Guided reassembly
    • Controller and source map
  • Guided reassembly
    • Start with one target
    • What runs
    • Resources and outputs
  • Parameters and interpretation
    • Sequence and similarity settings
    • Parameter selection
    • Manual overrides and fresh runs
  • Output files
  • Resources and reruns
    • Local execution
    • Reusing outputs and forcing a fresh run
  • CLI reference
    • recruit
    • info
    • Guided reassembly
  • Troubleshooting
  • Software and method citations

Maintaining SCARAB

  • Packaging, validation, and releases
    • One dependency definition
    • Validate this checkout
    • Build a local Conda package
    • Python artifacts
    • Configure publishing once
    • Build candidates without publishing
    • Publish an approved release
    • Shared controls with MetaPathways
    • Manual Zenodo archiving
  • Build and host this guide
    • Local preview
    • Read the Docs administration
    • Workflow figures
    • Workflow figures
SCARAB
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