Pinello Lab · Onboarding Automation Scripts

A cross-platform toolkit that turns a blank laptop and a brand-new Linux cluster account into a fully-configured development environment in minutes.

Script	Platform	What it does
scripts/local/onboarding_local_mac.sh	macOS 12 +	Installs VS Code + extensions, generates SSH keys, writes SSH config, then triggers the remote bootstrapper.
scripts/local/onboarding_local_windows.ps1	Windows 10/11	Same as mac, plus optional WSL 2 install & networking tweaks.
scripts/remote/onboarding_remote.sh	Cluster (Debian/Ubuntu)	Adds shared software to PATH, sets up Mamba/Conda, personal env folder, Jupyter password, VS Code server settings, and fixes SSH permissions.

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Repository layout

onboarding/
├── README.md
├── LICENSE
└── scripts/
    ├── local/
    │   ├── onboarding_local_mac.sh
    │   └── onboarding_local_windows.ps1
    └── remote/
        └── onboarding_remote.sh

Everything runnable lives in scripts/. Local scripts call the remote script via a relative path, so you can clone anywhere and just run.

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1 · Prerequisites

macOS	Windows	Remote Linux
Bash 3.x + (pre-installed)	PowerShell 5 + (or pwsh)	SSH access to ml007.research.partners.org
Git	Git & [winget]	Write access to ~/.bashrc
—	(Optional) admin rights for WSL install	—

Mac note You may be prompted to install Apple’s Command-Line Tools (Git/SSH) on first use.

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2 · Clone the repo

git clone https://github.com/pinellolab/onboarding.git
cd onboarding

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3 · Run the local script

macOS

chmod +x scripts/local/onboarding_local_mac.sh
./scripts/local/onboarding_local_mac.sh

Windows (PowerShell)

Set-ExecutionPolicy -Scope Process -ExecutionPolicy Bypass
.\scripts\local\onboarding_local_windows.ps1

During execution you can choose to:

1. Install Microsoft Teams and VS Code (plus WSL 2 on Windows).
2. Install VS Code extensions Remote-SSH, Python, Jupyter, Copilot.
3. Generate an SSH key (if missing) and copy it to the cluster.
4. Provide your MGH username so the script can run the remote bootstrapper.

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4 · What the remote script does

onboarding_remote.sh runs on the first cluster host you connect to and:

• Adds /data/pinello/SHARED_SOFTWARE/bin to PATH.
• Initialises Mamba + Conda and creates a personal envs directory.
• Optionally sets a Jupyter Lab password (v 2.16).
• Writes fresh VS Code Machine settings so the Python extension auto-selects the shared Miniforge interpreter.
• Ensures ~/.ssh/authorized_keys exists and has the correct permissions.

Re-running the script is safe & idempotent – no duplicate lines or conflicts.

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5 · Troubleshooting

Symptom	Fix
code CLI not found (mac)	Launch VS Code once and run “Shell Command: Install ‘code’ command in PATH”, or export PATH="/Applications/Visual Studio Code.app/Contents/Resources/app/bin:$PATH".
winget not recognised (Win)	Install the Windows Package Manager from the Microsoft Store or upgrade to Windows 10 21H2 / Windows 11.
Permission denied (publickey) on SSH	Re-run the local script; ensure the key was generated and ssh-copy-id succeeded.
VS Code on server shows no interpreter	Connect once, then Python → Select Interpreter and pick the Miniforge3 entry ending in /bin/python.

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6 · Updating / contributing

1. Fork or branch off main.
2. Edit scripts inside scripts/.
3. Run shellcheck on .sh and Invoke-ScriptAnalyzer on .ps1.
4. Open a pull request — CI will run the linters automatically.

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7 · License

Distributed under the MIT License — see LICENSE for details.

Happy on-boarding 🎉