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Setup

Environment management uses uv with Python 3.11+.

Quick Setup

git clone https://github.com/docxology/metainformant.git
cd metainformant
bash scripts/package/setup.sh --ncbi-email "you@example.com"
# Default setup installs dev + scientific dependencies + amalgkit
# You can either use uv run directly, or activate the venv for the shell:
# uv run python -V
source .venv/bin/activate  # or /tmp/metainformant_venv/bin/activate on FAT filesystems

Note: Setup scripts automatically detect FAT filesystems (exFAT, FAT32) and configure UV cache and virtual environment locations accordingly. See UV Setup Guide for details.

FAT Filesystem Support

On FAT-formatted external drives, setup is automatic:

# Same command works on FAT filesystems
bash scripts/package/setup.sh

# The script automatically:
# - Detects FAT filesystem
# - Sets UV_CACHE_DIR=/tmp/uv-cache
# - Creates venv at /tmp/metainformant_venv (if needed)

See UV Setup Guide for complete FAT filesystem documentation.

Verify Setup

# Standard verification
uv run python -V
uv run pytest -q
uv run metainformant --help

# Comprehensive verification (includes FAT filesystem checks)
bash scripts/package/verify.sh --mode setup

Directories policy

  • config/: repository-level configuration and options; read via metainformant.core.config with environment overrides.
  • data/: datasets and local databases (inputs), organized by domain/version.
  • output/: all outputs from tests and real runs. Ephemeral and reproducible; safe to delete.

Examples respect this policy by defaulting to output/ when writing files.

External tools

  • RNA: amalgkit (installed automatically by default setup script, via uv)
  • Optional MSA: muscle or clustalo in PATH (MUSCLE shim installed automatically if not found)
  • Optional NCBI Datasets: ncbi-datasets-pylib is a dependency; verify availability in runtime

Next steps