superbio 0.1.9

Python client for the Superbio API

Superbio Python Client

Official Python client for the Superbio platform API. Access bioinformatics tools and AI models programmatically.

Installation

pip install superbio

Quick Start

from superbio import Client

# Initialize client
client = Client("[e-mail]", "your_password")

# List available apps
apps = client.get_app_list()

# Get app parameters
app_params = client.get_app_parameters("app_id")

# Submit a job with local files
job = client.post_job(
    app_id="app_id",
    running_mode="cpu",
    config={"param": "value"},
    local_files={"file_key": "path/to/file"}
)

Submit a job with S3 files

job = client.post_job(
    app_id="app_id",
    running_mode="cpu",
    config={"param": "value"},
    remote_file_source_data={
        "file_key": [{
            "protocol": "s3",
            "credentials": {
                "aws_access_key_id": "YOUR_ACCESS_KEY",
                "aws_secret_access_key": "YOUR_SECRET_KEY"
            },
            "path": "bucket/path/to/file.csv"
        }]
    }
)

Check job status

status = client.get_job_status("job_id")

Download results

client.download_job_results("job_id", "output_directory")

Features

• Browse and search available bioinformatics applications
• Get detailed app configurations and parameters
• Submit computational jobs with:
  • Local files
  • Remote files (S3)
  • Files from Superbio DataHub
• Monitor job status and progress
• Download and manage results
• Track credit balances and usage

Authentication

You must first create an account at app.superbio.ai. Your email and password from the platform will be used to authenticate API requests.

Examples

Working with Apps

# Get list of all apps
apps = client.get_app_list()

# List apps with pagination and search
apps = client.get_app_list(
    hits_per_page=10,  # (optional) Number of results per page
    page=1,            # (optional) Page number
    search_string="genomics"  # (optional)Search by keyword
)

# Get app details and parameters
app_config = client.get_app_parameters("app_id")

Job Management

# List jobs with filters
jobs = client.get_jobs(
    hits_per_page=100,           # (optional) Number of jobs per page
    page=1,                      # (optional) Page number
    status="running",            # (optional) Filter by status: "running", "completed", "failed", etc.
    date_from="01/01/2024",      # (optional) Filter by start date (dd/mm/yyyy)
    date_to="31/01/2024",        # Filter by end date (dd/mm/yyyy)
    search_string="analysis"     # Search job titles
)

# Download specific result files
client.download_job_result_file(
    job_id="job_id",
    file_path="path/to/result.csv",  # Path of file in job results
    path_to_download_to="output_dir",         # Local directory to save file
)

# Download all results
client.download_all_job_results(
    job_id="job_id",
    path_to_download_to="output_dir",     # Local directory to save files
)

# Delete a job
client.delete_job("job_id")

Credit Management

# Get credit balances and usage info
balances = client.get_balances()
# Returns:
# {
#     "balances": {
#         "available_credits": 6000,
#         "credits": 6000,
#         "runs_left": 400,
#         "total_runs": 400,
#         "runtime_left": 72000.0,
#         "total_runtime": 72000,
#         "runs_reset_time": "Feb 28 2025, 23:08:05",
#         "runtime_reset_time": "Feb 28 2025, 23:08:05",
#         "tier": "free_organisation"
#     }
# }

Support

For support, contact [e-mail].