`oxo-flow env`#

Manage software environments. Provides subcommands for listing available backends and checking workflow environment requirements.

Usage#

oxo-flow env <SUBCOMMAND>

Subcommands#

`env list`#

List available environment backends, or list environments defined in a workflow.

oxo-flow env list [WORKFLOW]

When called without arguments, lists all backends detected on the system. When given a workflow file, lists the environments used by each rule.

Output:

oxo-flow v0.23.2 — Rust-native bioinformatics pipeline engine
https://github.com/Traitome/oxo-flow
Available environment backends:
  ✓ conda
  ✓ docker
  ✓ singularity
  ✓ venv

The two banner lines print only at an interactive terminal. All of this output goes to stderr — capture it with 2> or 2>&1; stdout stays empty.

`env check`#

Check that all environments declared in a workflow file are valid and their backends are available.

oxo-flow env check [WORKFLOW]

Argument	Description
`[WORKFLOW]`	Optional path to the `.oxoflow` workflow file. If omitted, checks system-wide backend availability instead.

Output (all valid):

  ✓ align (conda)
  ✓ call_variants (docker)
  ✓ annotate (singularity)

Without a workflow, each available backend also names the binary that a run would resolve — the engine prefers mamba → micromamba → conda, so on a machine with several conda-family installs the resolved binary is what actually gets invoked:

Environment backend availability:
  ✓ mamba (resolved: micromamba)
  ✓ conda
  ✗ docker (not found)

`env create`#

Create a new environment from a specification file.

oxo-flow env create [OPTIONS] <SPEC>

Argument	Description
`<SPEC>`	Path to the environment specification file (`.yaml`/`.yml`, `.toml`, `.lock`)

Option	Short	Description
`--name`	`-n`	Custom name for the created environment (default: derived from the spec filename)
`--ai`	—	Generate the environment spec from a natural-language description (SPEC is the description)
`--backend`	—	Environment backend to generate: conda (YAML) or pixi (TOML). Default: inferred from the spec's extension, or conda with `--ai`

Output (missing backend):

  ✓ align (conda)
  ✗ call_variants — environment error (docker): docker is not installed or not in PATH

Options#

Option	Short	Description
`--verbose`	`-v`	Enable debug-level logging

Examples#

# List available backends
oxo-flow env list

# Check a specific workflow
oxo-flow env check pipeline.oxoflow

Notes#

env check exits with code 1 if any environment validation fails
The check verifies backend availability, not that specific conda environments or Docker images exist — it confirms that the required type of environment manager is installed
Run env check before submitting to a cluster to catch environment issues early
To check that environment definition files exist (conda YAML, venv directories, pixi.toml), use oxo-flow test --deep (finding D002)

oxo-flow env#