🚧 wip(hello_seqera): first pass at interactive compute envs

.devcontainer/devcontainer.json

@@ -1,6 +1,8 @@
 {
     "name": "nfcore",
-    "image": "ghcr.io/nextflow-io/training:latest",
+    "build": {
+        "dockerfile": "../.github/gitpod.Dockerfile"
+    },
     "remoteUser": "gitpod",
     "features": {
         "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
@@ -23,7 +25,7 @@
                 "ms-python.vscode-pylance",
                 "nf-core.nf-core-extensionpack",
                 "nextflow.nextflow",
-                "codezombiech.gitignore",
+                "codezombiech.gitignore"
             ]
         }
     },

docs/hello_nextflow/10_hello_seqera.md

@@ -12,9 +12,7 @@ In this section, we'll introduce you to Seqera Platform, a powerful cloud-based
 
     [Sign up](https://cloud.seqera.io/) to try Seqera for free or request a [demo](https://seqera.io/demo/) for deployments in your own on-premise or cloud environment.
 
-You'll learn how to use Seqera Platform within Nextflow CLI, the Seqera Platform GUI, and the API.
-
-You can use Seqera Platform via either the **CLI**, through the **online GUI** or through the **API**.
+You'll learn how to use Seqera Platform within Nextflow CLI command-line interface, the Seqera Platform GUI (Graphical User Interface), and the Seqera API (Application Program Interface).
 
 --8<-- "docs/hello_nextflow/seqera/01_run_with_cli.md"
 

docs/hello_nextflow/seqera/01_run_with_cli.md

@@ -33,7 +33,7 @@ Follow these steps to set up your token:
     Open a terminal and type:
 
     ```bash
-    export TOWER_ACCESS_TOKEN=eyxxxxxxxxxxxxxxxQ1ZTE=
+     export TOWER_ACCESS_TOKEN=eyxxxxxxxxxxxxxxxQ1ZTE=
     ```
 
     Where `eyxxxxxxxxxxxxxxxQ1ZTE=` is the token you have just created.
@@ -84,30 +84,31 @@ Before we set the configuration, we need to permanently store the token in Nextf
 nextflow secrets set tower_access_token "eyxxxxxxxxxxxxxxxQ1ZTE="
 ```
 
-The following block of configuration will enable Seqera Platform logging by default:
+We want to configure Nextflow to use Seqera Platform by default across all our pipelines, so we will open the global Nextflow configuration file (`$HOME/.nextflow/config`) for editing:
 
-```groovy title="nextflow.config"
-tower {
-    enabled = true
-    endpoint = "https://api.cloud.seqera.io"
-    accessToken = secrets.tower_access_token
-}
+```bash
+code $HOME/.nextflow/config
 ```
 
-However, instead of enabling Seqera Platform for an individual pipeline, we want to enable it for ourselves globally.
-
-Run the following command to put the config block in your user configuration file located at `$HOME/.nextflow/config`.
+Add the following configuration to the file:
 
-```bash
-cat <<EOF >> $HOME/.nextflow/config
+```groovy title="$HOME/.nextflow/config"
 tower {
     enabled = true
-    endpoint = "https://api.cloud.seqera.io"
     accessToken = secrets.tower_access_token
+    workspaceId = secrets.tower_workspace_id
+    endpoint = "https://api.cloud.seqera.io"
 }
-EOF
 ```
 
+!!! hint "Workspace ID and Endpoint`
+
+    We haven't set `secrets.tower_workspace_id` yet, and so Nextflow will fill in an empty string for this value.
+    This will default to the user's workspace in Seqera Platform which is what we want for now.
+
+    The `endpoint` is the URL of the Seqera Platform API.
+    If your institution is running a private instance of Seqera Platform, you will want to change this to the appropriate URL.
+
 Run your Nextflow workflows as usual:
 
 ```bash

docs/hello_nextflow/seqera/03_add_compute_environment.md

@@ -23,4 +23,73 @@ To practice this process, we will simulate setting up a new slurm compute enviro
 
 ### 3.1. Setup Tower Agent
 
-### 3.2. Add a new Slurm compute environment
+Most Seqera compute environments require provisioning a [credential](https://docs.seqera.io/platform/latest/credentials/overview) that grants access to those compute resources.
+In this case, we will use [Tower Agent ](https://docs.seqera.io/platform/24.1/supported_software/agent), a lightweight program that can be installed on any machine to enable Seqera Platform to run Nextflow workflows on your behalf.
+
+Follow these instructions to configure your Tower Agent.
+
+    1. Create a new Token named "GitpodAgentToken" on the tokens page, following previous instructions.
+    1. Export your token into your current terminal:
+
+        ```bash
+         export TOWER_ACCESS_TOKEN=<your-token>
+        ```
+
+    1. Within Seqera Platform, click on your workspace name on the top left, and change back to your personal user workspace.
+    1. Click on the "Credentials" tab
+    1. Add the name "gitpodTowerAgent" to the name field
+    1. Select "Tower Agent" from the list of providers.
+    1. Copy the "Agent Connection ID" shown in the dropdown, it should look similar to `75d74f5f-9454-48b6-8967-cf20b74f6c78`
+    1. In your terminal execute the command below replacing with your connection ID:
+
+        ```bash
+        tw-agent 75d74f5f-9454-48b6-8967-cf20b74f6c78 --work-dir=./work
+        ```
+
+    1. Return to Seqera Platform and click on the "Add" button.
+
+If you completed this successfully, you'll see "gitpodTowerAgent" in the list of credentials in Seqera Platform, and console output in your terminal similar to what's below:
+
+```console title="tw-agent logs"
+21:47:33.531 INFO - Established active environments: [cli]
+21:47:33.662 INFO - TOWER AGENT v0.5.0
+21:47:33.662 INFO - Compatible with TOWER API v1.8
+21:47:33.662 INFO - Connecting as user 'gitpod' with default work directory '/workspaces/training/work'
+21:47:34.565 INFO - Connecting to Tower
+21:47:34.801 INFO - Connection to Tower established
+21:48:18.674 INFO - Sending heartbeat
+21:48:18.755 INFO - Received heartbeat
+21:49:03.680 INFO - Sending heartbeat
+21:49:03.741 INFO - Received heartbeat
+```
+
+### 3.2. Add a _simulated_ Grid Engine compute environment to Seqera Plaform.
+
+Now that we have set up a credential granting us secure access to our computational resources, we will set up a Compute Environment in Seqera which is a set of configuration that allows us to launch nextflow pipelines.
+Follow the steps below:
+
+    1. Navigate to the Compute Environments tab of Seqera Platform.
+    1. Click "Add compute environment"
+    1. Name your compute environment `gitpodGridEngine`.
+    1. Select "Grid Engine" as the target execution platform.
+    1. Make sure "gitpodTowerAgent" is selected from the list of credentials.
+    1. Click "Add"
+
+### 3.3. Add a pipeline to the launchpad for execution on our "Compute Environment"
+
+Now we need to set up a pipeline in Seqera Platform to run on our simulated Grid Engine compute environment.
+
+Follow the steps below:
+
+    1. Click on the "Launchpad" tab of Seqera Platform.
+    1. On the top right click on "Add Pipeline".
+    1. For name enter `hello-grid-engine`
+    1. For the Compute Environment select `gitpodGridEngine`
+    1. For the "Pipeline to launch" enter `nextflow-io/hello`.
+    1. Finally click "Add"
+
+You now should see "hello-grid-engine` in the list of pipelines.
+
+### 3.4. Launch your Nextflow pipeline
+
+To create that:

mkdocs.yml

@@ -155,6 +155,8 @@ markdown_extensions:
           preserve_tabs: true
     - pymdownx.tabbed:
           alternate_style: true
+    - pymdownx.tasklist:
+          custom_checkbox: true
     - tables
     - toc:
           title: On this page