Installation

Installation

Conda installation (recommended)

conda create -n sga-tools \
  -c conda-forge \
  -c bioconda \
  --strict-channel-priority \
  sar11-genome-atlas-tools
conda activate sga-tools

Verify the installation:

sga-db --version
sga-mapper --version
sga-classify --version
sga-run --version

PyPI installation

The Python package is also available from PyPI:

python -m pip install sar11-genome-atlas-tools

PyPI does not install Prodigal, HMMER, EPA-ng, fastANI, MAFFT, or FastTree. Those native executables must be installed separately and available on PATH.

Runtime database cache

Missing assets are downloaded from the SGAtools Zenodo record and stored under:

~/.cache/sga-tools/

Set SGA_CACHE_DIR to use another location, for example:

export SGA_CACHE_DIR=/scratch/$USER/sga-tools-cache

Use --no-download to require that all needed assets already exist.

See Example Tests for reproducible commands using the public FAA and FNA files in the GitHub repository.