biotailor 0.1.14

Python SDK for the Biotailor bioinformatics pipeline platform

biotailor

Python SDK for the Biotailor bioinformatics pipeline platform.

Table of Contents

• Installation
• Quickstart
• API Reference
  • Client: BiotailorClient
    • Tool discovery
    • Dataset discovery
    • Job management
    • Running and monitoring pipelines
  • Tools: ToolConfig
  • Pipelines: Pipeline
  • Models
  • Exceptions
• Development
• Publishing to PyPI

Installation

pip install biotailor

Quickstart

from biotailor import BiotailorClient, Pipeline

# 1. Create a client (get your API key from the Biotailor website)
client = BiotailorClient(api_key="btk_xxx.sk_yyy")

# 2. Discover available tools
client.print_tools()

# 3. Build a pipeline
tool = client.get_tool("fastp-single")

pipeline = (
    Pipeline(name="QC my reads", tool=tool)
    .set_input("input", "reads.fastq")
    .set_param("qualified_quality_phred", 20)
)

# 4. Run and wait
job = client.run_and_wait(pipeline, output_dir="./results")
print(f"Job {job.jobid} finished with status: {job.job_status.value}")

API Reference

Import the main SDK objects from biotailor:

from biotailor import BiotailorClient, Pipeline

Client: BiotailorClient

Create one client per API key. By default, it uses the production API at https://api.biotailor.org.

client = BiotailorClient(
    api_key="btk_xxx.sk_yyy",
    base_url="https://api.biotailor.org",
    timeout=30,
    debug=False,
)

Tool discovery

Method	Returns	Description
list_tools()	list[ToolConfig]	Fetch all available tool configurations.
get_tools()	list[ToolConfig]	Alias for list_tools().
print_tools()	None	Print all tools as a human-readable table.
get_tool(tool_id)	ToolConfig	Fetch one tool by ID, such as "fastp-single" or "bowtie2".

Dataset discovery

Method	Returns	Description
list_datasets(type=None)	list[Dataset]	Fetch available datasets, optionally filtered by dataset type.
print_datasets(type=None)	None	Print datasets grouped by dataset type.

Example:

client.print_datasets(type="bowtie2_db")
datasets = client.list_datasets()

Job management

Method	Returns	Description
list_jobs(sortBy="latestStatusTimestamp", order="desc", jobNameFilter=None)	list[Job]	Fetch jobs, with optional sorting and name filtering.
print_jobs(sortBy="latestStatusTimestamp", order="desc", jobNameFilter=None)	None	Print jobs as a human-readable table.
get_job(job_id)	Job	Fetch current status and metadata for one job.
cancel_job(job_id)	None	Cancel a running job.

sortBy supports "latestStatusTimestamp" and "startTimestamp". order supports "asc" and "desc".

Running and monitoring pipelines

Method	Returns	Description
run(pipeline, show_progress=True)	Job	Create a job, submit the workflow, upload input files, and return the initial job.
wait_for_completion(job_id, poll_interval=10, timeout=None, verbose=True)	Job	Poll until the job reaches a terminal status. Prints status updates and running logs when verbose=True.
run_and_wait(pipeline, output_dir=None, poll_interval=10, timeout=None, show_progress=True)	Job	Convenience method that runs a pipeline, waits for completion, and optionally downloads outputs on success.
get_job_logs(job_id, process_id)	str	Fetch formatted logs for a specific process in a job.
get_output_file_sizes(job_id)	list[dict]	Fetch output file size metadata for a completed job.
download_outputs(job_id, output_dir, process_id=None, show_progress=True)	list[str]	Download output files for all processes, or one process if process_id is provided.

Tools: ToolConfig

ToolConfig describes one Biotailor tool. You usually get it from client.get_tool() or client.list_tools().

Important fields:

Field	Description
toolid	Tool identifier used by the API.
display_name	Human-readable tool name.
category	Tool category, such as quality control or alignment.
description	Optional long-form tool description.
has_sepe	Whether the tool supports both single-end and paired-end modes.
default_hardware	Default DefaultHardware with CPU and RAM settings.
parameters	List of ToolParameter objects.
outputs	List of Output objects.

Methods:

Method	Returns	Description
tool_guide()	str	Return a readable guide with tool info, parameters, outputs, and sample pipeline code.
print_tool_guide()	None	Print the same guide returned by tool_guide().

Example:

tool = client.get_tool("bowtie2")
tool.print_tool_guide()

Pipelines: Pipeline

Pipeline is a chainable builder for one tool run. Pass either a ToolConfig object or a tool ID string.

pipeline = Pipeline(name="my-job", tool=tool)

Builder methods:

Method	Returns	Description
set_param(param_id, value)	Pipeline	Set one non-file tool parameter.
set_params(**kwargs)	Pipeline	Set multiple non-file parameters at once.
set_input(param_id, file_path)	Pipeline	Set one local file input.
set_input_batch(param_id, file_paths)	Pipeline	Set multiple local files for a batch input.
set_dataset(param_id, dataset_type, dataset_id)	Pipeline	Use a platform dataset as an input source.
set_hardware(cpu, ram_gb)	Pipeline	Override default hardware. CPU must be one of the supported powers of two; RAM must be cpu * 2, cpu * 4, or cpu * 8.
set_pair_end()	Pipeline	Mark the run as paired-end. Required for tools that support both single-end and paired-end modes.
set_single_end()	Pipeline	Mark the run as single-end. Required for tools that support both single-end and paired-end modes.

Utility methods:

Method	Returns	Description
validate(available_datasets=None)	None	Validate file paths, hardware, required parameters, parameter value types, SE/PE mode compatibility, and optional dataset catalog matches.
build_workflow(available_datasets=None)	dict	Build the workflow JSON sent to the API. Calls validate() first.
get_file_map()	dict[str, str]	Return the local file map used by the uploader.
has_dataset_inputs()	bool	Return whether the pipeline uses any platform datasets.

For tools with has_sepe=True, always call either set_single_end() or set_pair_end() before running.

Models

The SDK uses dataclasses for API responses and tool definitions.

Model	Purpose	Key fields
Job	Job metadata and status.	jobid, job_name, job_status, start_timestamp, latest_status_timestamp, end_timestamp, estimate_cost, processes_name, workflow, raw
JobStatus	Job status enum.	BUILDING, UPLOADING, STARTING, RUNNING, FAILED, SUCCEEDED, CANCELLED; use JobStatus.terminal_statuses() for terminal states.
Dataset	Platform dataset metadata.	dataset_id, display_name, description, dataset_type, compression_method, s3uri, raw
ToolConfig	Full tool configuration.	toolid, display_name, category, has_sepe, default_hardware, parameters, outputs, description
ToolParameter	One configurable tool input or parameter.	id, display_name, type, description, default_value, validation, is_pair_end_only, is_single_end_only, alias
Validation	Validation rules for a parameter.	required, minimum, maximum, options, accepted_input_types, accepted_compression_method
Option	One allowed option for a parameter.	display_name, value, description
Output	One declared tool output.	id, display_name, description, file_type, file_name, compression_method, is_pair_end_only, is_single_end_only, alias
DefaultHardware	Default tool hardware.	cpu, ram_in_gb

Exceptions

All SDK exceptions inherit from BiotailorError.

Exception	When it is raised
BiotailorAPIError	The API returns a non-2xx response. Includes status_code, message, and response_body.
BiotailorValidationError	Client-side validation fails before a request or upload.
BiotailorUploadError	Uploading an input file fails.

Development

# Install in dev mode
pip install -e ".[dev]"

# Run tests
pytest tests/ -v

# Lint
ruff check src/ tests/

Publishing to PyPI

# 1. Install build tools
pip install build twine

# 2. Clean old builds and build the package
rm -rf dist/
python -m build

# 4. Upload to PyPI
twine upload dist/*

Note: Bump version in pyproject.toml before each release — PyPI rejects duplicate versions. Use a PyPI API token for authentication (username: __token__).