seqerakit

seqerakit is a Python wrapper for the Seqera Platform CLI. It can be leveraged to automate the creation of all of the entities in Seqera Platform via a simple configuration file in YAML format.

The key features are:

• Simple configuration: All of the command-line options available when using the Seqera Platform CLI can be defined in simple YAML format.
• Infrastructure as Code: Enable users to manage and provision their infrastructure specifications.
• Automation: End-to-end creation of entities within Seqera Platform, all the way from adding an Organization to launching pipeline(s) within that Organization.

Prerequisites

You will need to have an account on Seqera Platform (see Plans and pricing).

Installation

seqerakit requires the following dependencies:

1. Seqera Platform CLI (>=0.9.2)

2. Python (>=3.8)

3. PyYAML

Conda

You can install seqerakit and its dependencies via Conda. Ensure that you have the correct channels configured:

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

You can then create a conda environment with seqerakit installed using the following:

conda env create -n seqerakit seqerakit
conda activate seqerakit

Pip

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

pip install seqerakit

You can force overwrite the installation to use the latest changes with the command below:

pip install --upgrade --force-reinstall seqerakit

Local development installation

You can install the development branch of seqerakit on your local machine to test feature updates of the tool. Before proceeding, ensure that you have Python and Git installed on your system.

1. To install directly from pip:

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

2. Alternatively, you may clone the repository locally and install manually:

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

You can verify your installation with:

pip show seqerakit

Configuration

Create a Seqera Platform access token using the Seqera Platform web interface via the Your Tokens page in your profile.

seqerakit reads this token from the environment variable TOWER_ACCESS_TOKEN. Please export it into your terminal as shown below:

export TOWER_ACCESS_TOKEN=<Your access token>

For Enterprise installations of Seqera Platform, you will also need to configure the API endpoint that will be used to connect to the Platform. You can do so by exporting the following environment variable:

export TOWER_API_ENDPOINT=<Tower API URL>

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

Usage

To confirm the installation of seqerakit, configuration of the Seqera Platform CLI and connection to the Platform is working as expected. This will run the tw info command under the hood:

seqerakit --info

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

seqerakit --help

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

seqerakit --version

Input

seqerakit supports input through either file paths to YAMLs or directly from standard input (stdin).

Using File Path

seqerakit /path/to/file.yaml

Using stdin

$ cat file.yaml | seqerakit -

See the Defining your YAML file using CLI options section for guidance on formatting your input YAML file(s).

Dryrun

To print the commands that would executed with tw when using a YAML file, you can run seqerakit with the --dryrun flag:

seqerakit file.yaml --dryrun

Recursively delete

Instead of adding or creating resources, you can recursively delete resources in your YAML file by specifying the --delete flag:

seqerakit file.yaml --delete

For example, if you have a YAML file that defines an Organization -> Workspace -> Team -> Credentials -> Compute Environment that have already been created, with the --delete flag, seqerakit will recursively delete the Compute Environment -> Credentials -> Team -> Workspace -> Organization.

Using tw specific CLI options

tw specific CLI options can be specified with the --cli= flag:

seqerakit file.yaml --cli="--arg1 --arg2"

You can find the full list of options by running tw -h.

The Seqera Platform CLI expects to connect to a Seqera Platform instance that is secured by a TLS certificate. If your Seqera Platform Enterprise instance does not present a certificate, you will need to qualify and run your tw commands with the --insecure flag.

To use tw specific CLI options such as --insecure, use the --cli= flag, followed by the options you would like to use enclosed in double quotes.

For example:

seqerakit file.yaml --cli="--insecure"

For Seqera Platform Enterprise, to use an SSL certificate that is not accepted by the default Java certificate authorities and specify a custom cacerts store as accepted by the tw CLI, you can specify the -Djavax.net.ssl.trustStore=/absolute/path/to/cacerts option enclosed in double quotes to seqerakit as you would to tw, preceded by --cli=.

For example:

seqerakit hello-world-config.yml --cli="-Djavax.net.ssl.trustStore=/absolute/path/to/cacerts"

Note: Use of --verbose option for the tw CLI is currently not supported by seqerakit. Supplying --cli="--verbose" will raise an error.

Specify targets

When using a YAML file as input that defines multiple resources, you can use the --targets flag to specify which resources to create. This flag takes a comma-separated list of resource names.

For example, given a YAML file that defines the following resources:

workspaces:
  - name: 'showcase'
    organization: 'seqerakit_automation'
...
compute-envs:
  - name: 'compute-env'
    type: 'aws-batch forge'
    workspace: 'seqerakit/test'
...
pipelines:
  - name: "hello-world-test-seqerakit"
    url: "https://github.com/nextflow-io/hello"
    workspace: 'seqerakit/test'
    compute-env: "compute-env"
...

You can target the creation of pipelines only by running:

seqerakit test.yml --targets pipelines

This will process only the pipelines block from the YAML file and ignore other blocks such as workspaces and compute-envs.

Multiple Targets

You can also specify multiple resources to create by separating them with commas. For example, to create both workspaces and pipelines, run:

seqerakit test.yml --targets workspaces,pipelines

YAML Configuration Options

There are several options that can be provided in your YAML configuration file, that are handled specially by seqerakit and/or are not exposed as tw CLI options.

1. Pipeline parameters using params and params-file

To specify pipeline parameters, you may either use params: to specify a list of parameters, or use params-file: to point to a parameters file.

For example, to specify pipeline parameters within your YAML:

params:
  outdir: 's3://path/to/outdir'
  fasta: 's3://path/to/reference.fasta'

Alternatively, to specify a file containing pipeline parameters:

params-file: '/path/to/my/parameters.yaml'

Optionally, you may provide both:

params-file: '/path/to/my/parameters.yaml'
params:
  outdir: 's3://path/to/outdir'
  fasta: 's3://path/to/reference.fasta'

Note: If duplicate parameters are provided, the parameters provided as key-value pairs inside the params nested dictionary of the YAML file will take precedence over values in the provided params-file.

2. overwrite Functionality

For every entity defined in your YAML file, you can specify overwrite: True to overwrite any existing entities in Seqera Platform of the same name.

seqerakit will first check to see if the name of the entity exists, if so, it will invoke a tw <subcommand> delete command before attempting to create it based on the options defined in the YAML file.

DEBUG:root: Overwrite is set to 'True' for organizations

DEBUG:root: Running command: tw -o json organizations list
DEBUG:root: The attempted organizations resource already exists. Overwriting.

DEBUG:root: Running command: tw organizations delete --name $SEQERA_ORGANIZATION_NAME
DEBUG:root: Running command: tw organizations add --name $SEQERA_ORGANIZATION_NAME --full-name $SEQERA_ORGANIZATION_NAME --description 'Example of an organization'

3. Specifying JSON configuration files with file-path

The Seqera Platform CLI allows export and import of entities through JSON configuration files for pipelines and compute environments. To use these files to add a pipeline or compute environment to a workspace, use the file-path key to specify a path to a JSON configuration file.

An example of the file-path option is provided in the compute-envs.yml template:

compute-envs:
  - name: 'my_aws_compute_environment'                              # required
    workspace: 'my_organization/my_workspace'                       # required
    credentials: 'my_aws_credentials'                               # required
    wait: 'AVAILABLE'                                               # optional
    file-path: './compute-envs/my_aws_compute_environment.json'     # required
    overwrite: True

Quick start

You must provide a YAML file that defines the options for each of the entities you would like to create in Seqera Platform.

You will need to have an account on Seqera Platform (see Plans and pricing). You will also need access to a Workspace and a pre-defined Compute Environment where you can launch a pipeline.

Launch via YAML

1. Create a YAML file called hello-world-config.yml with the contents below, and customise the <YOUR_WORKSPACE> and <YOUR_COMPUTE_ENVIRONMENT> entries as required:

   launch:
     - name: 'hello-world'                              # Workflow name
       workspace: '<YOUR_WORKSPACE>'                    # Workspace name
       compute-env: '<YOUR_COMPUTE_ENVIRONMENT>'        # Compute environment
       revision: 'master'                               # Pipeline revision
       pipeline: 'https://github.com/nextflow-io/hello' # Pipeline URL

2. Launch the pipeline with seqerakit:

   seqerakit hello-world-config.yml

3. Login to your Seqera Platform instance and check the Runs page in the appropriate Workspace for the pipeline you just launched!

Launch via a Python script

You can also launch the same pipeline via a Python script. This will essentially allow you to extend the functionality on offer within the Seqera Platform CLI by leveraging the flexibility and customisation options available in Python.

1. Download the launch_hello_world.py Python script and customise the <YOUR_WORKSPACE> and <YOUR_COMPUTE_ENVIRONMENT> entries as required.

2. Launch the pipeline with seqerakit:

   python launch_hello_world.py

3. Login to your Seqera Platform instance and check the Runs page in the appropriate Workspace for the pipeline you just launched!

Defining your YAML file using CLI options

All available options to provide as definitions in your YAML file can be determined by running the Seqera Platform CLI help command for your desired entity.

1. Retrieve CLI Options

To obtain a list of available CLI options for defining your YAML file, use the help command of the Seqera Platform CLI. For instance, if you want to configure a pipeline to be added to the Launchpad, you can view the options as follows:

$ tw pipelines add -h

Usage: tw pipelines add [OPTIONS] PIPELINE_URL

Add a workspace pipeline.

Parameters:
*     PIPELINE_URL                         Nextflow pipeline URL.

Options:
* -n, --name=<name>                        Pipeline name.
  -w, --workspace=<workspace>              Workspace numeric identifier (TOWER_WORKSPACE_ID as default) or workspace reference as OrganizationName/WorkspaceName
  -d, --description=<description>          Pipeline description.
      --labels=<labels>[,<labels>...]      List of labels seperated by coma.
  -c, --compute-env=<computeEnv>           Compute environment name.
      --work-dir=<workDir>                 Path where the pipeline scratch data is stored.
  -p, --profile=<profile>[,<profile>...]   Comma-separated list of one or more configuration profile names you want to use for this pipeline execution.
      --params-file=<paramsFile>           Pipeline parameters in either JSON or YML format.
      --revision=<revision>                A valid repository commit Id, tag or branch name.
  ...

2. Define Key-Value Pairs in YAML

Translate each CLI option into a key-value pair in the YAML file. The structure of your YAML file should reflect the hierarchy and format of the CLI options. For instance:

pipelines:
  - name: 'my_first_pipeline'
    url: 'https://github.com/username/my_pipeline'
    workspace: 'my_organization/my_workspace'
    description: 'My test pipeline'
    labels: 'yeast,test_data'
    compute-env: 'my_compute_environment'
    work-dir: 's3://my_bucket'
    profile: 'test'
    params-file: '/path/to/params.yaml'
    revision: '1.0'

In this example:

• name, url, workspace, etc., are the keys derived from the CLI options.
• The corresponding values are user-defined

Best Practices:

• Ensure that the indentation and structure of the YAML file are correct - YAML is sensitive to formatting.
• Use quotes around strings that contain special characters or spaces.
• When listing multiple values (labels, instance-types, allow-buckets, etc), separate them with commas as shown above.
• For complex configurations, refer to the Templates provided in this repository.

Templates

We have provided template YAML files for each of the entities that can be created on Seqera Platform. These can be found in the templates/ directory and should form a good starting point for you to add your own customization:

• organizations.yml
• teams.yml
• workspaces.yml
• participants.yml
• credentials.yml
• secrets.yml
• compute-envs.yml
• actions.yml
• datasets.yml
• labels.yml
• pipelines.yml
• launch.yml

Real world example

Please see seqerakit-e2e.yml for an end-to-end example that highlights how you can use seqerakit to create everything sequentially in Seqera Platform all the way from creating a new Organization to launching a pipeline.

You can modify this YAML to similarly create Seqera Platform resources end-to-end for your setup. This YAML encodes environment variables to protect sensitive keys, usernames, and passwords that are required to create or add certain resources (i.e. credentials, compute environments). Prior to running it with seqerakit examples/yaml/seqerakit-e2e.yml, you will have to set the following environment variables:

$TOWER_GITHUB_PASSWORD
$DOCKERHUB_PASSWORD
$AWS_ACCESS_KEY_ID
$AWS_SECRET_ACCESS_KEY
$AWS_ASSUME_ROLE_ARN
$AZURE_BATCH_KEY
$AZURE_STORAGE_KEY
$GOOGLE_KEY
$SENTIEON_LICENSE_BASE64

Contributions and Support

If you would like to contribute to seqerakit, please see the contributing guidelines.

For further information or help, please don't hesitate to create an issue in this repository.

Credits

seqerakit was written by Esha Joshi, Adam Talbot and Harshil Patel from the Scientific Development Team at Seqera Labs.