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2. Orientation

This workshop should be completed using the Nextflow Training Gitpod Environment.

Gitpod offers a virtual machine with everything already set up for you, accessible from your web browser or built into your code editor (e.g., VSCode).

To get started quickly, click on the button below.

Open in Gitpod

2.1 Running Gitpod

To run Gitpod:

Getting Started with GitHub

To get started with GitHub, you will need to create a free personal account on github.com and verify your email address.

Every person who uses github.com signs in to a personal account. Your account is your identity and has a username and profile.

Signing up for a new personal account:

  1. Navigate to https://github.com/.
  2. Click Sign up at the top right corner.
  3. Follow the prompts to create your account.

When you first sign up to Gitpod you may need to authenticate your account and supply some additional details.

2.1.1 Explore your Gitpod IDE

After Gitpod has loaded, you should now see something similar to the following:

Gitpod welcome

  • The sidebar allows you to customize your Gitpod environment and perform basic tasks (copy, paste, open files, search, git, etc.). You can click the explorer button to see which files are in this repository.
  • The terminal allows you to run all the programs in the repository. For example, both nextflow and docker are installed and can be executed.
  • The file explorer allows you to view and edit files. Clicking on a file in the explorer will open it within the main window.
  • The Simple Browser lets you view the nf-training material browser (https://training.nextflow.io/). If you close it by accident, you can load the simple browser again by typing the following in the terminal: gp preview https://training.nextflow.io.

2.1.2 Gitpod resources

  • Gitpod gives you 500 free credits per month, which is equivalent to 50 hours of free environment runtime using the standard workspace (up to 4 cores, 8 GB RAM, and 30 GB storage).
  • There is also a large workspace option that gives you up to 8 cores, 16GB RAM, and 50GB storage. However, the large workspace will use your free credits quicker and you will have fewer hours of access to this space.
  • Gitpod will time out after 30 minutes of inactivity and will save your changes for up to 2 weeks.

More information about Gitpod is available at gitpod.io.

2.1.3 Reopening a Gitpod session

You can reopen an environment from https://gitpod.io/workspaces. Previous environments will be listed. You can select the ellipsis (three dots icon) and then select Open to reopen a previous environment.

If you have saved the URL for your previous Gitpod environment, you can simply open it in your browser.

Alternatively, you can open a new training workspace by following the Gitpod URL: https://gitpod.io/#https://github.com/nextflow-io/training

2.1.4 Saving files from Gitpod to your local machine

To save any file from the explorer panel, right-click the file and select Download.

2.2 Getting started

The Gitpod environment contains some test data that will be used in this workshop.

Move to the nf-customize folder to get started.

Exercise

Open the Gitpod training environment and use the following command to switch to the empty nf-customize folder:

cd /workspace/gitpod/nf-customize