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* Add Gitpod qmd (#48) * gitpod login instructions * gitpod login * remove names * Update gitpod.qmd - Gitpod uses (#52) * what is gitpod (#56) * what is gitpod * Update gitpod.qmd Adding a sentence about the ".gitpod.yml" file * Update section on configuration in gitpod.qmd (#60) * edit_how_to_start_agitpod.qmd (#51) * Update Schedule * Update schedule * Add Git cheetsheet (#43) * Add quarto introduction lecture * Add learner/review pairs * Update Render vs Preview * Update intro.qmd * Add section on quarto computatations * Apply code review fixes for Quarto syntax * Add reference in figure example * Update intro.qmd - The Quarto CLI initial commit section: The Quarto CLI * Add section on document formats * Update quarto/intro.qmd Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * Update quarto/intro.qmd Co-authored-by: Mahesh Binzer-Panchal <[email protected]> * apptainer.qmd rough lesson plan * example.def * Update apptainer.qmd * add runscript to example .def file * lesson notes * Update apptainer.qmd * add Mahesh notes * Update Schedule (#65) * Add chapter on pixi (#68) * Add chapter on pixi * incorporated the other changes suggested by mahesh-panchal * Update Pixi lesson * Move gitpod intro * Organise chapters * Update Gitpod Intro * Remove extra space --------- Co-authored-by: CormacKinsella <[email protected]> Co-authored-by: Jason Hill <[email protected]> Co-authored-by: Estelle PW <[email protected]> Co-authored-by: Guilherme Borges Dias <[email protected]> Co-authored-by: Miguel Ángel Redondo <[email protected]> Co-authored-by: Per Unneberg <[email protected]> Co-authored-by: Martin Pippel <[email protected]> Co-authored-by: Amrei <[email protected]>
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| # Gitpod | ||
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| ## What is Gitpod | ||
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| [Gitpod](https://gitpod.io) is a developer environment that runs in your browser. In order to use it, you need a Git repository (either on GitHub, GitLab or Bitbucket). Gitpod opens up a container on your Git repository and clones the repository to the developer environment. This developer environment is initialized from the file `.gitpod.yml` present in the repository. | ||
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| There are two offerings of Gitpod, Gitpod Flex, and Gitpod Enterprise. Gitpod Flex is designed to run a container on your laptop, cloud, or on-premises architecture. Gitpod Enterprise, which we discuss here, runs on a cloud environment hosted by Gitpod. | ||
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| There are different pricing depending on your needs such as: | ||
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| - Free plan (50 hours per month) | ||
| - Pay-as-you-go | ||
| - Company plan (custom) | ||
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| Mahesh is on an open source plan (nammed NBIS). NBIS does not pay for a Gitpod plan or allow Gitpod to push directly to the NBISweden organization. Contributions to repositories on NBISweden must be made by Pull Request from your personal fork of a repository. Gitpod can then be run on your own forked repositories through your personal authentication. | ||
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| ## How to login to Gitpod | ||
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| - Go to the [Gitpod site](https://gitpod.io). | ||
| - Select your Git hosting service (e.g., GitHub), and authenticate. | ||
| - If successful you should land on the workspaces page, with organisation settings at top left, and personal settings at top right. | ||
| - Now when you start a Gitpod environment you'll be connected to your version control system. | ||
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| ## How to start a Gitpod | ||
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| To start a workspace, follow these steps: | ||
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| - Navigate to your repository on GitHub, GitLab or Bitbucket. | ||
| - Add `gitpod.io/#` before the URL address of your repository. This will create a new URL address that directs you to the Gitpod workspace setup page. On that page, you can make the following choices: | ||
| 1. The source repository for which the gitpod workspace will be created. | ||
| 2. The code editor. | ||
| 3. The computing resources required for the workspace. | ||
| - After making your choices, the code editor will open, allowing the user can start working on the files in the repository. The user's working directory is a cloned folder of the Github repository located on the Gitpod server, not locally on the computer. | ||
| - Any changes to the files within that folder can be pushed to the repository using Git commands. | ||
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| **Note**: If you are editing a public Github public repository, Gitpod requires the "public_repo" permission to push changes. To do it, follow these steps: | ||
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| 1. Navigate to gitpod.io. | ||
| 2. Click on your user icon | ||
| 3. Click "user settings" | ||
| 4. Navigate to "Git Providers" | ||
| 5. Click the actions icon on the GitHub provider | ||
| 6. Click "edit permissions" | ||
| 7. Check "public_repo" | ||
| 8. Click "Update permissions" | ||
| 9. You will be redirected to Github for authentication. | ||
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| After granting permissions, the user can push changes to the repository. | ||
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| ## How to configure Gitpod | ||
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| - A gitpod workspace is configured mainly through the `.gitpod.yml` file at the root of your repository (e.g. github.com/user/repo/.gitpod.yml). | ||
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| - This file is read by Gitpod when the workspace is started, and can be used to specify the base workspace image, and a list of tasks that will be run when the workspace is started. | ||
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| - Below is the yml file we use in the Training-tech-shorts repo. | ||
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| ```yml | ||
| image: nfcore/gitpod:latest | ||
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| tasks: | ||
| - name: Update Nextflow | ||
| command: nextflow self-update | ||
| - name: Install Pixi | ||
| command: | | ||
| sudo chown gitpod -R /home/gitpod/ | ||
| curl -fsSL https://pixi.sh/install.sh | bash | ||
| . /home/gitpod/.bash_profile | ||
| - name: Install Quarto | ||
| command: | | ||
| wget https://quarto.org/download/latest/quarto-linux-amd64.deb | ||
| sudo dpkg -i quarto-linux-amd64.deb | ||
| rm quarto-linux-amd64.deb | ||
| quarto check all | ||
| ``` | ||
| - The `image:` section of the `.gitpod.yml` is used to specify the base workspace image, this can be a public or private docker image, or a Dockerfile (in this case the base image must be public). | ||
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| ```yml | ||
| # public image | ||
| image: nfcore/gitpod:latest | ||
| # local Dockerfile | ||
| image: | ||
| file: .gitpod.Dockerfile | ||
| ``` | ||
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| - The `tasks:` section of the `.gitpod.yml` is used to specify a list of tasks that will be run when the workspace is started. Each task should have a `name:` and a `command:` section. The `command:` section specifies one or more shell commands that will be run in the workspace. | ||
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| ```yml | ||
| tasks: | ||
| - name: Update Nextflow | ||
| command: nextflow self-update | ||
| ``` | ||
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| - In order to execute multiple commands in a single task, you can use the `|` syntax to specify a block of shell commands, each in one line. | ||
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| ```yml | ||
| tasks: | ||
| - name: Install Pixi | ||
| command: | | ||
| sudo chown gitpod -R /home/gitpod/ | ||
| curl -fsSL https://pixi.sh/install.sh | bash | ||
| . /home/gitpod/.bash_profile | ||
| ``` | ||
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| - Optionally, you can also add a `ports:` section to the `.gitpod.yml` file to specify a list of ports that should be opened by the workspace. This can be useful when hosting a web server or anything that needs to be accessed from outside the workspace. | ||
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| ```yml | ||
| ports: | ||
| - port: 8080 | ||
| onOpen: open-preview | ||
| ``` | ||
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| ## Uses for Gitpod | ||
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| - Demonstration: The containerized nature of gitpod makes it useful for serving instances of a program in a standardized environment for demonstration. | ||
| - Development: There are many software development tools available in the standard docker container. Pull requests can be managed from within gitpod and explored safely within a container. | ||
| - Experimentation: The ephemeral nature of the environment, and its standardized tools make Gitpod excellent for testing code and sandbox experimentation. | ||
| - Training: A pre-built environment can be provided to learners and supplies a consistent environment to work in with the necessary lesson requirements. |
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