Seqerakit docs port

platform_versioned_docs/version-24.1/seqerakit/commands.mdx

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+---
+title: "Commands"
+description: "seqerakit command options"
+date: "21 Oct 2024"
+tags: [seqerakit, cli, automation, commands]
+---
+
+Use the `--help` or `-h` parameter to list available commands and options:
+
+```bash
+seqerakit --help
+```
+
+### Input
+
+`seqerakit` supports input through paths to YAML configuration files or directly from standard input (stdin).
+
+- Using file path:
+
+    ```bash
+    seqerakit /path/to/file.yaml
+    ```
+
+- Using stdin:
+
+    ```console
+    $ cat file.yaml | seqerakit -
+    ```
+
+See [Define your YAML file using CLI options](#define-your-yaml-file-using-cli-options) for guidance on formatting your input YAML files.
+
+### Dryrun
+
+Confirm that your configuration and command are correct before creating resources in your Seqera account, particularly when automating the end-to-end creation of multiple entities at once. To print the commands that would be executed with Platform CLI when using a YAML file, run your seqerakit command with the `--dryrun` flag:
+
+```bash
+seqerakit file.yaml --dryrun
+```
+
+### Specify targets
+
+When using a YAML file as input that defines multiple resources, use the `--targets` flag to specify which resources to create. This flag accepts a comma-separated list of resource names.
+
+For example, given a `test.yml` file that defines the following resources:
+
+```yaml
+workspaces:
+  - name: 'workspace-1'
+    organization: 'seqerakit'
+...
+compute-envs:
+  - name: 'compute-env'
+    type: 'aws-batch forge'
+    workspace: 'seqerakit/workspace-1'
+...
+pipelines:
+  - name: "hello-world"
+    url: "https://github.com/nextflow-io/hello"
+    workspace: 'seqerakit/workspace-1'
+    compute-env: "compute-env"
+...
+```
+
+You can target the creation of `pipelines` only by running:
+
+```bash
+seqerakit test.yml --targets pipelines
+```
+
+This will process only the pipelines block from the YAML file and ignore `workspaces` and `compute-envs`.
+
+To create both workspaces and pipelines, run:
+
+```bash
+seqerakit test.yml --targets workspaces,pipelines
+```
+
+### Delete resources
+
+Instead of adding or creating resources, specify the `--delete` flag to recursively delete resources in your YAML file:
+
+```bash
+seqerakit file.yml --delete
+```
+
+For example, if you have a `file.yml` that defines an organization, workspace, team, credentials, and compute environment that have already been created, run `seqerakit file.yml --delete` to recursively delete the same resources.
+
+### Use `tw`-specific CLI options
+
+Specify `tw`-specific CLI options with the `--cli=` flag:
+
+```bash
+seqerakit file.yaml --cli="--arg1 --arg2"
+```
+
+See [CLI commands](../cli/commands.mdx) or run `tw -h` for the full list of options.
+
+:::note
+The `--verbose` option for `tw` CLI is currently not supported by `seqerakit`.
+:::
+
+#### Example: HTTP-only connections
+
+The Platform CLI expects to connect to a Seqera instance that is secured by a TLS certificate. If your Seqera Enterprise instance does not present a certificate, you must 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 to use enclosed in double quotes:
+
+```bash
+seqerakit file.yaml --cli="--insecure"
+```

platform_versioned_docs/version-24.1/seqerakit/installation.mdx

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+---
+title: "Installation"
+description: "seqerakit installation options"
+date: "21 Oct 2024"
+tags: [seqerakit, cli, automation, installation]
+---
+
+
+`seqerakit` is a Python wrapper that sets [Platform CLI](../cli/overview.mdx) command options using YAML configuration files. Individual seqerakit 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 (`>=0.9.2`)](https://github.com/seqeralabs/tower-cli/releases)
+2. [Python (`>=3.8`)](https://www.python.org/downloads/)
+3. [PyYAML](https://pypi.org/project/PyYAML/)
+
+#### Pip
+
+If you already have [Seqera Platform CLI](../cli/installation.mdx) and Python installed on your system, install `seqerakit` directly from [PyPI](https://pypi.org/project/seqerakit/):
+
+```console
+pip install seqerakit
+```
+
+Overwrite an existing installation to use the latest version:
+
+```console
+pip install --upgrade --force-reinstall seqerakit
+```
+
+#### Conda
+
+To install `seqerakit` and its dependencies via Conda, first configure the correct channels:
+
+```console
+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:
+
+```console
+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](https://www.python.org/downloads/) and [Git](https://git-scm.com/downloads) installed on your system.
+1. To install directly from pip:
+    ```bash
+    pip install git+https://github.com/seqeralabs/seqera-kit.git@dev
+    ```
+1. Alternatively, clone the repository locally and install manually:
+    ```bash
+    git clone https://github.com/seqeralabs/seqera-kit.git
+    cd seqera-kit
+    git checkout dev
+    pip install .
+    ```
+1. Verify your installation:
+    ```bash
+    pip show seqerakit
+    ```
+
+### Configuration
+
+Create a [Seqera](https://cloud.seqera.io/) access token via **Your Tokens** in the user menu.
+
+`seqerakit` reads your access token from the `TOWER_ACCESS_TOKEN` environment variable:
+
+```bash
+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:
+
+```bash
+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: 
+
+```bash
+seqerakit --info
+```
+
+This runs the `tw info` command under the hood.
+
+Use `--version` or `-v` to retrieve the current version of your `seqerakit` installation:
+
+```bash
+seqerakit --version
+```
+
+Use the `--help` or `-h` parameter to list the available commands and their associated options:
+
+```bash
+seqerakit --help
+```
+
+See [Commands](./commands.mdx) for detailed instructions to use `seqerakit`.

platform_versioned_docs/version-24.1/seqerakit/overview.mdx

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+---
+title: "Overview"
+description: "An overview of seqerakit"
+date: "10 Oct 2024"
+tags: [seqerakit, cli, automation]
+---
+
+`seqerakit` is a Python wrapper that allows you to set [Platform CLI](../cli/overview.mdx) command options with YAML configuration files. Individual seqerakit commands and configuration parameters can be chained together to automate the end-to-end creation of all Seqera Platform entities.
+
+### Key features
+
+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 Platform entities, from adding an organization to launching pipelines.
+
+### Availability
+
+seqerakit can be installed on macOS, Windows, and Linux. It is compatible with [Seqera Platform Cloud](https://cloud.seqera.io/) and Enterprise versions 21.08 and later.
+
+See [Installation](./installation.mdx) to get started.
+
+:::info
+You can also invoke and run `seqerakit` via a [Python script](https://github.com/seqeralabs/seqera-kit#launch-via-a-python-script).
+:::

platform_versioned_docs/version-24.1/seqerakit/quickstart.mdx

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+---
+title: "Quickstart"
+description: "seqerakit Hello World pipeline example"
+date: "21 Oct 2024"
+tags: [seqerakit, cli, automation, commands, hello world]
+---
+
+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 a Seqera account (see [Plans and pricing](https://seqera.io/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 customize the `<YOUR_WORKSPACE>` and `<YOUR_COMPUTE_ENVIRONMENT>` entries as needed:
+
+   ```yaml
+   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`:
+
+   ```bash
+   seqerakit hello-world-config.yml
+   ```
+
+3. Log in to your Seqera 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 allows you to extend Platform CLI functionality by leveraging the flexibility and customization options available in Python.
+
+1. Download the [`launch_hello_world.py`](./examples/python/launch_hello_world.py) Python script and customize the `<YOUR_WORKSPACE>` and `<YOUR_COMPUTE_ENVIRONMENT>` entries as needed.
+
+2. Launch the pipeline with `seqerakit`:
+
+```bash
+   python launch_hello_world.py
+```
+
+3. Log in to your Seqera instance and check the **Runs** page in the appropriate workspace for the pipeline you just launched. 
+