binchicken build

DESCRIPTION

Create dependency environments

OPTIONS

--singlem-metapackage SINGLEM_METAPACKAGE

SingleM metapackage

--checkm2-db CHECKM2_DB

CheckM2 database

--gtdbtk-db GTDBTK_DB

GTDBtk release database (Only required if --aviary-speed is set to {COMPREHENSIVE_AVIARY_MODE})

--metabuli-db METABULI_DB

MetaBuli database (Only required with TaxVAMB extra binner)

--set-tmp-dir SET_TMP_DIR

Set temporary directory [default: /tmp]

--skip-aviary-envs

Do not install Aviary subworkflow environments

--build-gpu

Build GPU-friendly environments for certain binners in Aviary recovery [default: do not]. Must be run on a node with GPU access.

--download-databases

Download databases if provided paths do not exist

--output OUTPUT

Output directory [default: .]

--cores CORES

Maximum number of cores to use [default: 1]

--dryrun

dry run workflow

--snakemake-profile SNAKEMAKE_PROFILE

Snakemake profile (see https://snakemake.readthedocs.io/en/v7.32.3/executing/cli.html#profiles). Can be used to submit rules as jobs to cluster engine (see https://snakemake.readthedocs.io/en/v7.32.3/executing/cluster.html).

--local-cores LOCAL_CORES

Maximum number of cores to use on localrules when running in cluster mode [default: 1]

--cluster-retries CLUSTER_RETRIES

Number of times to retry a failed job when using cluster submission (see `--snakemake-profile`) [default: 3].

--snakemake-args SNAKEMAKE_ARGS

Additional commands to be supplied to snakemake in the form of a space- prefixed single string e.g. " --quiet"

--tmp-dir TMP_DIR

Path to temporary directory. [default: no default]

OTHER GENERAL OPTIONS

--debug

output debug information

--version

output version information and quit

--quiet

only output errors

--full-help

print longer help message

--full-help-roff

print longer help message in ROFF (manpage) format

EXAMPLES

create dependency environments

$ binchicken build

create dependency environments and setup environment variables for databases

$ binchicken build --singlem-metapackage metapackage --checkm2-db CheckM2 --gtdbtk-db GTDBtk

create dependency environments and download databases

$ binchicken build --singlem-metapackage metapackage --checkm2-db CheckM2 --download-databases