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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 all environment backends available on the current system.

oxo-flow env list

Output:

oxo-flow 0.1.0 — 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> Path to the .oxoflow workflow file

Output (all valid):

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

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#

# 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