Installation

Seqerakit is a Python wrapper that sets Platform CLI command options using YAML configuration files. Individual commands and configuration parameters can be chained together to automate the end-to-end creation of all Seqera Platform entities.

As an extension of the Platform CLI, Seqerakit enables:

• Infrastructure as code: Users manage and provision their infrastructure from the command line.
• Simple configuration: All Platform CLI command-line options can be defined in simple YAML format.
• Automation: End-to-end creation of Seqera entities, from adding an organization to launching pipelines.

Installation

Seqerakit has three dependencies:

1. Seqera Platform CLI (>=0.10.1)
2. Python (>=3.8)
3. PyYAML

Pip

If you already have Platform CLI and Python installed on your system, install Seqerakit directly from PyPI:

pip install seqerakit

Overwrite an existing installation to use the latest version:

pip install --upgrade --force-reinstall seqerakit

Conda

To install seqerakit and its dependencies via Conda, first configure the correct channels:

conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

Then create a conda environment with seqerakit installed:

conda env create -n seqerakit seqerakit
conda activate seqerakit

Local development installation

Install the development branch of seqerakit on your local machine to test the latest features and updates:

1. You must have Python and Git installed on your system.
2. To install directly from pip:

   pip install git+https://github.com/seqeralabs/seqera-kit.git@dev

3. Alternatively, clone the repository locally and install manually:

   git clone https://github.com/seqeralabs/seqera-kit.git
   cd seqera-kit
   git checkout dev
   pip install .

4. Verify your installation:

   pip show seqerakit

Configuration

Create a Seqera access token via Your Tokens in the user menu.

Seqerakit reads your access token from the TOWER_ACCESS_TOKEN environment variable:

export TOWER_ACCESS_TOKEN=<Your Seqera access token>

For Enterprise installations, specify the custom API endpoint used to connect to Seqera. Export the API endpoint environment variable:

export TOWER_API_ENDPOINT=<Seqera Enterprise API URL>

By default, this is set to https://api.cloud.seqera.io to connect to Seqera Cloud.

Usage

To confirm the installation of seqerakit, configuration of the Platform CLI, and connection to Seqera is working as expected, run this command:

seqerakit --info

This runs the tw info command under the hood.

Use --version or -v to retrieve the current version of your seqerakit installation:

seqerakit --version

Use the --help or -h option to list the available commands and their associated options:

seqerakit --help

See Commands for detailed instructions to use Seqerakit.