biolm protocol

biolm protocol cancel

Request cancellation of protocol RUN_ID.

Usage

biolm protocol cancel [OPTIONS] RUN_ID

Options

--format <output_format>

Output format.

Default:

'table'

Options:

table | json

Arguments

RUN_ID

Required argument

biolm protocol download

Download result artifacts for successful protocol RUN_ID.

Usage

biolm protocol download [OPTIONS] RUN_ID

Options

--output-dir <output_dir>

Directory for the downloaded zip.

Default:

'.'

--file-type <file_type>

Default:

'csv'

Options:

csv | jsonl

--overwrite

Replace an existing download.

Arguments

RUN_ID

Required argument

biolm protocol init

Create a new protocol YAML file from a blank template or bundled example.

Generated files can be validated immediately with biolm protocol validate.

Usage

biolm protocol init [OPTIONS] [FILENAME]

Options

-o, --output <output>

Output file path (default: protocol.yaml)

-e, --example <example>

Use an example template

--list-examples

List available example templates

-f, --force

Overwrite existing file

-i, --interactive

Interactive mode to select example

Arguments

FILENAME

Optional argument

biolm protocol list

List protocols registered on the BioLM platform.

Usage

biolm protocol list [OPTIONS]

Options

--search <search>

Filter protocols by name or slug.

--page <page>

Default:

1

--page-size <page_size>

Default:

20

--format <output_format>

Output format.

Default:

'table'

Options:

table | json

biolm protocol log

Log protocol run results to MLflow using the protocol outputs configuration.

Creates or updates an experiment at account/workspace/protocol and records metrics, parameters, and artifacts from a results file.

Usage

biolm protocol log [OPTIONS] RESULTS

Options

--outputs <outputs>

Outputs config YAML or protocol YAML file

--account <account>

Required Account name (experiment path: account/workspace/protocol)

--workspace <workspace>

Required Workspace name (experiment path: account/workspace/protocol)

--protocol <protocol_slug>

Required Protocol name/slug (experiment path: account/workspace/protocol)

--dry-run

Prepare data without logging to MLflow

--mlflow-uri <mlflow_uri>

MLflow tracking URI

--aggregate-over <aggregate_over>

Compute aggregates over selected rows or all rows

Options:

selected | all

--protocol-name <protocol_name>

Protocol display name for metadata (default: from protocol YAML)

--protocol-version <protocol_version>

Protocol version for metadata

Arguments

RESULTS

Required argument

biolm protocol results

Show or save results for protocol RUN_ID.

Usage

biolm protocol results [OPTIONS] RUN_ID

Options

--output <output>

Write the full run detail as JSON instead of printing it.

--format <output_format>

Terminal output format.

Default:

'json'

Options:

table | json

Arguments

RUN_ID

Required argument

biolm protocol run

Submit a run of registered protocol SLUG.

Usage

biolm protocol run [OPTIONS] SLUG

Options

-i, --inputs <inputs_file>

JSON object containing protocol inputs. Use ‘-’ for stdin.

--version <version>

Protocol version.

--name <run_name>

Human-readable run name.

--environment-id <environment_id>

Environment ID to attribute the run to.

--wait

Wait for completion and print the full run result.

--timeout <timeout>

Total wait deadline in seconds.

Default:

3600.0

--poll-interval <poll_interval>

REST fallback polling interval in seconds.

Default:

5.0

--format <output_format>

Output format.

Default:

'table'

Options:

table | json

Arguments

SLUG

Required argument

biolm protocol run local

Execute a protocol YAML file locally via the pipeline runtime.

Requires biolm[pipeline]. Validates the protocol, compiles to a DataPipeline, runs tasks, and prints a summary (or JSON records with –json).

Usage

biolm protocol run-local [OPTIONS] PROTOCOL_FILE

Options

--input <input_pairs>

Input key=value (value parsed as JSON when possible)

--json

Output results as JSON records

--output-dir <output_dir>

Pipeline output directory

Arguments

PROTOCOL_FILE

Required argument

biolm protocol show

Show a formatted report for a protocol from a local YAML file or platform ID.

Displays tasks, dependencies, inputs/outputs, and configuration in a readable layout.

Usage

biolm protocol show [OPTIONS] [PROTOCOL_SOURCE]

Arguments

PROTOCOL_SOURCE

Optional argument

biolm protocol status

Show a current progress snapshot for protocol RUN_ID.

Usage

biolm protocol status [OPTIONS] RUN_ID

Options

--format <output_format>

Output format.

Default:

'table'

Options:

table | json

Arguments

RUN_ID

Required argument

biolm protocol validate

Validate a protocol YAML file against the JSON schema and internal rules.

Checks YAML syntax, task references, circular dependencies, and template expressions.

Usage

biolm protocol validate [OPTIONS] PROTOCOL_FILE

Options

--json

Output results in JSON format

Arguments

PROTOCOL_FILE

Required argument

biolm protocol wait

Wait for protocol RUN_ID and print its final detail.

Usage

biolm protocol wait [OPTIONS] RUN_ID

Options

--timeout <timeout>

Total wait deadline in seconds.

Default:

3600.0

--poll-interval <poll_interval>

REST fallback polling interval in seconds.

Default:

5.0

--format <output_format>

Output format.

Default:

'table'

Options:

table | json

Arguments

RUN_ID

Required argument