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Setup

Installation of the Basepair Python package and CLI.
Contents:

  1. Installation
  2. Configuration

1. Installation​

Requirements​

  • Python 3.8+ (Python 2 is no longer supported)

Install the package​

pip install basepair

Once installed, the basepair command should be available:

basepair -h

2. Configuration​

You need a configuration file to connect to Basepair’s API. To obtain it:

  1. Go to your dashboard: app.basepairtech.com
  2. Click the profile icon (top-right).
  3. Click Profile.
  4. Click Download API config file (upper-right).

A downloaded file looks like:

{
  "api_v3": {
    "cli": true,
    "host": "app.basepairtech.com",
    "prefix": "/api/v3/",
    "ssl": true,
    "username": "user@basepairtech.com",
    "key": "YOUR_API_KEY"
  }
}

key is your personal access token. The api_v3 section targets the current API (v3). If your downloaded file still shows an api section with /api/v2/, see the migration guide to update it.

Config keys and API versions​

The config section key determines which API version the SDK uses:

Config keyprefixAPI version
api_v3/api/v3/v3 (default since package 3.x)
api/api/v2/v2 (legacy)

You can keep both sections in the same file if you need to switch versions:

{
  "api_v3": {
    "host": "app.basepairtech.com",
    "prefix": "/api/v3/",
    "ssl": true,
    "username": "user@example.com",
    "key": "YOUR_V3_KEY"
  },
  "api": {
    "host": "app.basepairtech.com",
    "prefix": "/api/v2/",
    "ssl": true,
    "username": "user@example.com",
    "key": "YOUR_V2_KEY"
  }
}

To make this file available to your API calls, choose one of the following:

Option 1 – environment variable (recommended)

export BP_CONFIG_FILE=/path/to/basepair.config.json

Option 2 – command-line flag

basepair -c /path/to/basepair.config.json

Option 3 – environment variables only (no file needed)

export BP_USERNAME=user@basepairtech.com
export BP_API_KEY=YOUR_API_KEY

You can now use Basepair’s genomics tools from the CLI or the Python API.
For usage details, see the Command-Line API or Python API tutorials.

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