MetaPathways

Getting started

  • What MetaPathways does
  • Installation and first run
    • 1. Conda package with Mamba (preferred)
    • 2. Quay: Docker or Apptainer
    • 3. Local installation from GitHub
    • Try your own data
    • CAMI references
  • Getting started: from a terminal to your first result
    • What you will do
    • Before typing commands
    • Install on Linux x86-64
    • First installation check
    • Your first real assembly
    • Terms used in the guides
  • Quay containers: Docker and Apptainer
    • Docker three-sample test
    • Apptainer three-sample test
    • From the test to your own data
    • CAMI references
  • Test walkthrough: three tiny CAMI samples
    • 1. Install MP and prepare the small reference database
    • Run all three samples first
    • 2. Run the single-sample workflow
    • 3. Run two distinct samples together
    • 4. Check outputs and explore tables
    • 5. Optional: include licensed Pathway Tools
    • Provenance and validation
    • Recorded three-sample validation
    • CAMI references
  • Tiny CAMI II test inputs
    • Source attribution
    • CAMI references
  • Citing CAMI and CAMI II
    • CAMI references
    • Reference-manager download

Analysis guides

  • Organize assemblies, reads and genome assignments
    • Decide what each sample means
    • Automatic discovery
    • Organize with links, without copying large reads
    • Custom manifest: keep every file where it is
    • Contig-to-genome map format
  • Prepare reference databases
  • Pathway Tools: licensing, image builds, databases and inference
    • Defaults and explicit choices
    • Understand the three different databases
    • Get the installer
    • Host prerequisites
    • Build and register once
    • Build the MPDB MetaCyc annotation reference at the same time
    • Run pathway inference
    • Choose a taxonomic scope
    • Explicit reaction blacklist
    • Transport inference and sequence-backed inputs
    • Outputs, warnings and failures
    • Screen reaction compatibility (maintainers)
    • Intermittent container startup failures
  • Complete multi-sample analysis
    • Analysis wf input layout
    • Custom analysis manifest
    • Outputs, restarting and exploration
  • Annotate your own data
    • One assembly
    • Read mapping
    • Multiple assemblies
    • Stage controls
  • MAGs and pathway inference
    • Build Pathway Tools once
    • MetaCyc from Pathway Tools
    • Community pathways
    • Add MAG pathways without reannotating
  • Command cookbook: run only the modules you need
    • Choose a command
    • prepare_test: try the included data
    • build_db: references before analysis
    • run: annotations and optional abundance
    • analysis_wf: one complete run for N samples
    • mag_split: reuse community annotation
    • build_pt and ptools: licensed setup, then inference
    • report: inspect and export without reanalysis
    • Resources, failure and restart
  • Resources and Slurm
    • Local execution is the default
    • Submit from a Slurm headnode
  • Logs, temporary files and restarting
  • Troubleshooting and reproducibility

Results and reference

  • Explore results, follow links and export tables
    • Open the report or start the explorer
    • View a remote report through SSH
    • Start with accounting
    • Follow one annotation through the results
    • Select useful subsets
    • Avoid accidental double counting
    • Share or archive a result
  • Reports and the EDA portal
  • Results schema and EDA portal
    • What the report does
    • Relationships
    • Tables and their row units
    • Ready-made explorer views
    • Subsetting examples
    • Missing, partial and historical outputs
    • Outputs that stay as source files
    • Exports and local service
  • Software architecture: local and HPC
  • Data flow: inputs to connected results
  • Detailed workflow and tool citations
    • How to cite your analysis
    • 1. Prepare references and the optional Pathway Tools image
    • 2. Plan and schedule work
    • 3. Predict and annotate features
    • 4. Measure abundance, build PGDBs and assemble reports
    • Tool and wrapper index
    • Reference databases
    • Supporting software and distribution
    • Full references
  • Workflow and output guide
    • Command boundaries
    • Annotation stages
    • Output layout
    • Dependency and cache behavior
    • Report limitations and error recovery
  • Complete CLI reference
    • prepare_test
    • run
    • analysis_wf
    • build_db
    • mag_split
    • build_pt
    • screen_pt
    • ptools
    • report
  • Benchmarking and supplementary statistics
    • Define the experiment before starting
    • Example full workflow
    • What is recorded automatically
    • Supplementary table structure
    • Runtime and resource figures
    • Save environment and machine information
    • Finish, inspect, then summarize
    • Compare one server with a Slurm cluster
    • Compact results on limited storage
    • CAMI references
  • Reproducibility and validation
    • Record the actual revision and inputs
    • Installation example versus biological validation
    • Historical benchmark provenance
    • Documentation and release records
    • CAMI references

Development

  • PR tester checklist
    • CAMI references
  • Releasing MetaPathways
    • Normal release using GitHub CI
    • Shared release controls (MetaPathways and SCARAB)
    • Enable Anaconda.org uploads
    • Local build and validation
    • Rebuilds and failed releases
    • Recover the interrupted v3.5.0 GitHub upload
    • Docker, Apptainer, and Quay
    • Security rebuilds without changing the application version
    • Feature-branch review before publication
    • Zenodo and software citation
    • Account-side release checklist
    • CAMI references
  • MetaPathways 3.5.2 release readiness
    • Registry and container status
    • Completed checks
    • Before merge and public release
    • CAMI references
  • Maintaining the documentation
    • Build and review locally
    • Connect Read the Docs
    • Shared diagram scale
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