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Installation And Setup

Use the canonical runtime package when you want the main product surface.

Basic Route

  1. Install the runtime package.
  2. Confirm the CLI resolves.
  3. Run a small validation or inspection command.
  4. Keep local run products under artifacts/.

The operational goal is predictable local behavior, not hidden notebook state or scattered temporary outputs.

External Engine Runtime

Some workflows execute real scientific binaries rather than mock adapters. On macOS with Homebrew, install the current local engine set with:

make install-external-engine-runtime

That target installs:

  • mafft
  • trimal
  • iqtree2
  • FastTree
  • mb from MrBayes
  • beast from BEAST2

If you install those executables another way, make sure they resolve on PATH before you run the real local lanes.

Local Verification Routes

Use these commands when you want an executable-backed verification rather than the default lightweight surface:

make test-external-engines
make test-scientific-validation-slow
  • make test-external-engines Runs the compact real-engine integration lane plus the non-slow governed scientific-validation reruns.
  • make test-scientific-validation-slow Keeps the longer FASTA-to-tree reruns separate so they do not slow every local engine check.

The repository-owned make targets already route outputs into artifacts/ by default.