Environment setup

Bin Chicken uses separate conda environments for each subprocess. Run binchicken build to create those subprocess conda environments and setup environment variables.

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). Note that the databases are very large.

binchicken build \
  --conda-prefix /path/to/conda/envs/dir \
  --singlem-metapackage /metapackage/dir \
  --gtdbtk-db /gtdb/release/dir \
  --checkm2-db /checkm2/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 SNAKEMAKE_CONDA_PREFIX="/path/to/conda/envs"
conda env config vars set CONDA_ENV_PATH="/path/to/conda/envs"
conda env config vars set SINGLEM_METAPACKAGE_PATH="/metapackage/dir"
conda env config vars set GTDBTK_DATA_PATH="/gtdb/release/dir"
conda env config vars set CHECKM2DB="/checkm2/db/dir"