Environment setup

Bin Chicken uses separate conda environments for each subprocess. Run binchicken build to create those subprocess conda environments and setup environment variables. This can take upwards of 30 minutes to complete, depending on the speed of your internet connection.

Conda prefix is the directory you want to contain the subprocess conda environments. SingleM metapackage is the metapackage downloaded by SingleM using singlem data (see https://github.com/wwood/singlem).

The latter databases are required only if you want to run Aviary directly using the --run-aviary argument. GTDB-Tk database is the directory containing the GTDB-Tk release (see https://github.com/Ecogenomics/GTDBTk). CheckM2 database is the directory containing the CheckM2 database (see https://github.com/chklovski/CheckM2). These can also be downloaded automatically with --download-databases flag, which uses Aviary (aviary configure --download gtdb singlem checkm2, see https://github.com/rhysnewell/aviary). If you use this flag, note that it will only download the databases if the provided path does not already exist. Also note that the databases are very large.

binchicken build \
  --singlem-metapackage /metapackage/dir \
  --checkm2-db /checkm2/db/dir \
  # Optional: for use with Aviary comprehensive (`--aviary-speed comprehensive`)
  --gtdbtk-db /gtdb/release/dir \
  # Optional: for use with taxvamb extra binner (`--aviary-extra-binners taxvamb`)
  --metabuli-db /metabuli/db/dir

Alternatively, set directory to contain subprocess conda environments and environment variables manually. Subprocess conda environments will be created when required.

conda env config vars set SINGLEM_METAPACKAGE_PATH="/metapackage/dir"
conda env config vars set CHECKM2DB="/checkm2/db/dir"
# Optional: for use with Aviary comprehensive (`--aviary-speed comprehensive`)
conda env config vars set GTDBTK_DATA_PATH="/gtdb/release/dir"
# Optional: for use with taxvamb extra binner (`--aviary-extra-binners taxvamb`)
conda env config vars set METABULI_DB_PATH="/metabuli/db/dir"