Configuration¶

Environment variables¶

On first run, Aviary will prompt for database locations if they haven't been set. Use aviary configure to set or update them at any time:

aviary configure --gtdb-path /path/to/gtdb/ --checkm2-db-path /path/to/checkm2/

You can also set them manually in your .bashrc:

export GTDBTK_DATA_PATH=/path/to/gtdb/gtdb_release232/db/
export EGGNOG_DATA_DIR=/path/to/eggnog-mapper/2.1.3/
export SINGLEM_METAPACKAGE_PATH=/path/to/singlem/S6.5.0.GTDB_r232.metapackage_20260319.smpkg.zb
export CHECKM2DB=/path/to/checkm2db/uniref100.KO.1.dmnd

See aviary configure --help for all available options.

Thread control¶

Aviary has three thread control parameters:

-t, --max-threads

Controls how many threads any single program can use. If set to 24, each tool with threading support will use up to 24 threads.

-n, --n-cores

Controls total cores given to Snakemake. Setting this higher than --max-threads allows multiple rules to run concurrently. Defaults to match --max-threads if not set.

-p, --pplacer-threads

Pplacer gets its own parameter because it can deadlock with too many threads and is memory-intensive at high thread counts.

Example — run up to 4 rules in parallel:

aviary recover -1 reads_1.fq.gz -2 reads_2.fq.gz -t 8 -n 32

RAM control¶

Set maximum memory with -m/--max-memory (in gigabytes):

aviary recover -1 reads_1.fq.gz -2 reads_2.fq.gz -m 500

When using HPC cluster submission, requested job memory increases with each retry and is capped at --max-memory.

Note: GTDB-Tk v2.7.0+ requires at least 140 GB of RAM for R232.

Temporary directory¶

By default Aviary uses /tmp. To change it for a single run:

aviary recover -1 reads_1.fq.gz -2 reads_2.fq.gz --tmpdir /scratch/tmp/

To set it permanently:

aviary configure --tmpdir /scratch/tmp/