Русский

First Things First: What to do after the initial login to the server?

Nikita Vaulin, MedUni Wien & Bioinformatics institute
[email protected]

I had to repeat this so many times, so shall it be here in a clear and concise form. Feel free to share your thoughts in PR or in telegram

• 1. Authentication
  • 1.1. Changing password
  • 1.2. Setting up ssh-keys
• 2. Virtual environments
  • 2.1. Install mamba
  • 2.2. Create your first environment
• 3. Jupiter kernels
  • 3.1. Create Jupyter kernel
• 4. Conclusion

➡️ This you can just copy-paste-run
⏯️ This you need to copy-paste-EDIT-run
✔️ This is for check-up

1. Authentication

1.1. Changing password

Did your server admin create you user with default password? It's definetely worth changing it!

➡️ Just run:

passwd

And then follow the interactive menu (type old password, type new password, type new password once again)

✔️ Close Terminal and open once again, make sure you can log in into the server with your new password

1.2. Setting up ssh-keys

However if you are going to log in via ssh a lot (from Temrinal, or from VSCode, etc...) - it's better to make * ssh-keys*. I like these GitHub instruction. Long story short:

➡️ On your PC generate an ssh-key

ssh-keygen

(Options your might want to include: -t ed25519, -f ~/.ssh/<your_key_name>)

Then follow the interactive menu (just hit Enter to agree with everuthing unless you know what you want)

⏯️ Add the key to your agent:

eval "$(ssh-agent -s)"
ssh-add ~/.ssh/<your_key_name>

Then copy the whole content of the public part of your key (~/.ssh/<your_key_name>.pub), log in into the server with your password and add this content into the ~/.ssh/authorized_keys file on server (create if missing). Add means append as a new line, if file is already not empty.

⏯️ However, you can do it with a simple command:

cat ~/.ssh/<your_key_name>.pub | ssh <username>@<remote_host> "mkdir -p ~/.ssh && cat >> ~/.ssh/authorized_keys"

For more advanced experience consider creating an ssh-config file.

✔️ Close Terminal and open once again, make sure you can log in into the server without a password

2. Virtual environments

2.1. Install mamba

You may also use conda, but I prefer mamba. Follow Fresh install section.

➡️ In essence, download installation script and run it (just copy the commands)

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Hit Enter and type yes for any question.

✔️ Close Terminal and open once again, make sure you see the the (base) prefix in the command line

2.2. Create your first environment

Try not to install anything into your base environment.

⏯️ Run:

mamba create -n <your_env_name>

You may also add libraries you need:

mamba create -n <your_env_name> python=3.11 scanpy[leiden]

Then activate this environment

mamba activate <your_env_name>

✔️ Now you see your env name as a prefix in the command line ❓✔️⏯️➡️

3. Jupiter kernels

This part is relevant if your are going to use Jupyter Notebooks. I assume you have Jupyter Hub system which you can log in from the browser. Otherwise consider fresh jupyter installation.

3.1 Create Jupyter kernel

Now you have your mamba environment with the libraries your need. Let's make a jupyter kernel from this environment.

⏯️Get the library to manage kernels and make a kernel:

# For Python (run in Terminal)
pip install ipykernel
python -m ipykernel install --user --name <your_env_name>

# For R (run in R console)
install.packages('IRkernel')
IRkernel::installspec(user=TRUE, name='<your_env_name>')

✔️ Refresh the browser, now you will see an option to select your new kernel in the launcher.

Any new libraries in your environment will be automatically availble in this kernel!

4. Conclusion

That's it, we've made some initial server preparations. You're beautiful and good luck with your research!