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Configuration

atb stores its settings in ~/.config/atb/config.toml. Use atb config to create, view, and update them.

Create and view config

# Create default config
atb config init

# View config
atb config show

# Set the data directory (metadata index: parquet tables + SQLite)
atb config set general.data_dir /path/to/parquet/files

# Set where downloaded genomes go — a SEPARATE directory from the data dir
atb config set download.output_dir /path/to/genomes

# Set default download parallelism
atb config set download.parallel 8

Data directory vs download directory

general.data_dir is where atb fetch places the parquet tables and SQLite index. download.output_dir is where atb download writes genome FASTA files. They are independent — see Fetching & indexing data for details.

Shared installations (multi-user servers)

On a shared cluster you usually want every user to read from a single large data volume without each person editing their own config. Two env vars give an admin that without touching $HOME:

Variable Effect
ATB_DATA_DIR (alias: ATB_DATADIR) Overrides general.data_dir from the config file. Takes precedence over the config but loses to an explicit --data-dir flag.
ATB_CONFIG Path to the config file. Useful for shipping a site-wide config (e.g. /etc/atb/config.toml) via /etc/profile.d.

Example: drop a one-liner into /etc/profile.d/atb.sh and every login shell picks up the shared paths:

# /etc/profile.d/atb.sh
export ATB_DATA_DIR=/srv/atb/data
export ATB_CONFIG=/etc/atb/config.toml

Resolution order for the data directory is --data-dir flag → ATB_DATA_DIR env → config file → OS default.