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
Index
Index