Generating an SSH key

BioShell uses SSH key authentication. This guide walks you through generating a key pair, copying your public key, and submitting it to the BioShell Onboarding Portal.

Quick start

If you are familiar with SSH keys and just need the commands, use the steps below. For a full walkthrough including optional settings and troubleshooting, see the step-by-step guide below.

macOS and Linux

ssh-keygen -t ed25519 -C "your@email.com"

Press Enter three times to accept the defaults, then copy your public key:

cat ~/.ssh/id_ed25519.pub

Paste the output into the BioShell Onboarding Portal.

Windows

ssh-keygen -t ed25519 -C "your@email.com"

Press Enter three times to accept the defaults, then copy your public key:

cat $env:USERPROFILE\.ssh\id_ed25519.pub

Paste the output into the BioShell Onboarding Portal.

Prerequisites

Step 1: Generate the key pair

The recommended algorithm is Ed25519 — it is fast, secure, and compact. Use RSA 4096 only if a service requires it.

macOS and Linux

ssh-keygen -t ed25519 -C "your@email.com"

RSA fallback (legacy systems only):

ssh-keygen -t rsa -b 4096 -C "your@email.com"

Windows

ssh-keygen -t ed25519 -C "your@email.com"

RSA fallback:

ssh-keygen -t rsa -b 4096 -C "your@email.com"

Responding to prompts

After running the command you will see two prompts:

Enter file in which to save the key (/home/you/.ssh/id_ed25519):

Press Enter to accept the default path. If you use multiple keys across different systems, enter a custom path to keep them separate — for example:

/home/you/.ssh/id_ed25519_bioshell      # macOS and Linux
C:\Users\you/.ssh/id_ed25519_bioshell   # Windows

Your files will then be named id_ed25519_bioshell and id_ed25519_bioshell.pub. If you use a custom name, reference it explicitly when copying your public key (Step 4) and in your SSH config (see Managing multiple keys).

Enter passphrase (empty for no passphrase):

A passphrase encrypts your private key at rest. It is recommended for any key that will access production systems. Press Enter to skip.

Step 2: Verify the key files

After generation, two files are created:

macOS and Linux

ls -la ~/.ssh/

Windows

dir $env:USERPROFILE\.ssh\

Step 3: Add the key to ssh-agent (optional)

If you set a passphrase, the ssh-agent saves you from re-entering it every time you connect. Run the relevant command once after login:

Note: On macOS the key is stored in Keychain and persists across reboots. On Linux you may need to re-add the key after each session unless you configure your shell to start the agent automatically.

Step 4: Copy your public key

macOS

pbcopy < ~/.ssh/id_ed25519.pub

Or print it to copy manually:

cat ~/.ssh/id_ed25519.pub

Linux

# With xclip installed
xclip -selection clipboard < ~/.ssh/id_ed25519.pub

# Or print it to copy manually
cat ~/.ssh/id_ed25519.pub

Windows

# Copy to clipboard
Get-Content $env:USERPROFILE\.ssh\id_ed25519.pub | Set-Clipboard

# Or print it to copy manually
cat $env:USERPROFILE\.ssh\id_ed25519.pub

Step 5: Submit your public key to BioShell

1. Go to the BioShell Onboarding Portal.
2. Log in with your institutional credentials.
3. Paste your public key into the SSH Public Key field.
4. Submit the form — your account will be provisioned within [AUTHOR TO SUPPLY — add timeframe].

Your BioShell username will follow the convention firstname.lastname. Once your account is ready, return to the Connecting to BioShell section of the access guide.

Important: If you run into any issues, contact [AUTHOR TO SUPPLY — helpdesk email or link].

Managing multiple keys

Use ~/.ssh/config to assign different keys to different hosts:

Host bioshell
    HostName BIOSHELL_HOSTNAME
    User firstname.lastname
    IdentityFile ~/.ssh/id_ed25519_bioshell

Host github.com
    HostName github.com
    User git
    IdentityFile ~/.ssh/id_ed25519_github

With this config, connect to BioShell with ssh bioshell.

Note: On Windows this file lives at C:\Users\you\.ssh\config.

Key permissions (macOS and Linux)

SSH will refuse to use keys with overly permissive file modes. Fix incorrect permissions with:

chmod 700 ~/.ssh
chmod 600 ~/.ssh/id_ed25519
chmod 644 ~/.ssh/id_ed25519.pub
chmod 600 ~/.ssh/config           # if it exists
chmod 600 ~/.ssh/authorized_keys  # on servers

Adding a key later

If you need to register a new key (for example, from a new machine or after rotating an old key), use one of these options:

Option A: via the portal

Log back into the BioShell Onboarding Portal and add your new public key there.

Option B: directly on BioShell (if you still have access via an existing key)

cat ~/.ssh/id_ed25519.pub | ssh firstname.lastname@BIOSHELL_HOSTNAME \
  "cat >> ~/.ssh/authorized_keys"

Then verify correct permissions on the server:

ssh firstname.lastname@BIOSHELL_HOSTNAME "chmod 600 ~/.ssh/authorized_keys"

Testing your connection

ssh firstname.lastname@BIOSHELL_HOSTNAME

Use -v for verbose output when troubleshooting:

ssh -v firstname.lastname@BIOSHELL_HOSTNAME

Algorithm reference