Skip to content

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 0.6.1 — Bioinformatics Pipeline Engine
Available environment backends:
  ✓ conda
  ✓ docker
  ✓ singularity
  ✓ venv

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)

### `env create`

Create a new environment from a specification file.

```bash
oxo-flow env create <SPEC> [-n <NAME>]
Argument Description
<SPEC> Path to the environment specification file (.yaml, .toml, .lock)
Option Short Description
--name -n Custom name for the created environment (default: derived from the spec filename) 
**Output (missing backend):**
✓ align (conda)
✗ call_variants — Docker is not available on this system 
---

## Options

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

---

## Examples

```bash
# 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