deliablue / preparatoryweek_2023

This repository holds the material (documentation, activities and solutions) of the Bachelors degree of Bioinformatics 2nd course preparatory week. Course 2023-2024.

Welcome to the Preparatory Week 2023!

The 2nd course of the Bachelors Degree of Bioinformatics is the hardest one. During this year, you are going to face a lot of new and complicated material.

Do not suffer, we all have been there and succeeded. But because we know what it takes to do it, we know that these days we are going to share together are very important. Summer is coming to an end, and the last thing you want is to go back to classes and what's worst, classes before the official ones! We ask you to make an effort, this is really going to help you out.

Along the 10 scheduled hours we will cover vaguely how to work with GitHub and Vim. We will do a small introduction to C++ along with psuedocode. We will get a bit more technical by talking about memory allocation and its related errors in C++, ending each day with a little bit of Biopython.

It sounds like a lot and, in fact, it is. Knowing that, we will try to make it as easy for you to digest as possible and we you can always contact any of us at any time, we are more than glad to help. The content will be uploaded day after day, that's why you are seeing an empty repository. By the end of the week, all the material and activities done are going to be for you to keep and revisit.

With all this being said, we would like to welcome you to the beginning of the preparatory week. We hope you enjoy these days as much as we did preparing them!

Things To See Here

1. Installation and Configuration
   • Installation for The Penguin Club
   • Installation For The Half-apple Cult
2. The Coolest Team Ever!
   • The Juniors also Rock!

Installation

Linux

Prior to anything, I will suppose you already have Git installed. But just in case I am wrong (not an usual thing), you can make me be right with the following commands:

sudo apt-get update
sudo apt-get install git-all

To verify the installation (or just to check whether you have Git or not), type:

git version

In addition, for an easiest management (and other cool things that you can discover and play around with), GitHub CLI will also be installed with a super easy and simple command:

type -p curl >/dev/null || (sudo apt update && sudo apt install curl -y)
curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg \
&& sudo chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg \
&& echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
&& sudo apt update \
&& sudo apt install gh -y

Even if I'd really like to say that the next step is to clone this repository and start the fun part, there's a small thing left to do: the terrible and scary SSH key configuration.

Run the following command and change the email by the one you used to create a GitHub account (because you already have one right? If not... what are you waiting for?)

ssh-keygen -t ed25519 -C "[email protected]"

Afterwards, you will be asked to Enter a file in which to save the key. Just press Enter and use the default location (unless you are very anal and have the urge to use another file, then type it).
The next prompt will ask you to Enter passphrase; citing the GitHub docu:

With SSH keys, if someone gains access to your computer, the attacker can gain access to every system that uses that key. To add an extra layer of security, you can add a passphrase to your SSH key. To avoid entering the passphrase every time you connect, you can securely save your passphrase in the SSH agent.

I'm not going to cover that, you can refer to the official docu, I will proceed assuming you DID NOT Enter passphrase and just press Enter twice. In order to finish this terrible and scary part, you will add the SSH key you just generated to the ssh-agent and to your GitHub account.

Add SSH key to ssh-agent

eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

NOTE FOR FUSSY PEOPLE: If you have changed the SSH key filename, you will have to replace the id_ed25519 by the one you provided.

Add SSH key to you GitHub account

Okey, I might have told you a tiny little lie before when I told you that this was the last "small thing left to do", you must authenticate to the GitHub CLI in order to use it and add the SHH key. If I waited until this point is because I wanted to have the installation and configuration steps separated (and because I forgot it up there and I'm to lazy to fix it now).

To make the authentication, run the command

gh auth login

This command will lead you to an interrogation, but do not worry, I have the answers for you:

First Question: What account do you want to log into?
GitHub.com

Second Question: What is your preferred protocol for Git operations?
SSH

Third Question: Upload your SSH public key to your GitHub account?
/home/YOUR_USER_NAME/.ssh/id_ed25519.pub

Fourth Question: Title for your SSH key:
key_name

Last Question: How would you like to authenticate GitHub CLI?

• If you are a hero that has and remembers its token: Paste an authentication token

• If you are a mortal like me: Login with a web browser

Done! Finally it is time to have fun... or is it?

macOS

Let's deviate from the cool path, to make a small summary for the people that wrongly decided to join the half-apple cult (even though they made the wrong decision, we do not have to discriminate them).

Fruit-guys, I will assume that you have installed homebrew; if you do not, install it now. Again, in case you do not have Git installed in your computer, you can do it with the command

brew install git

As the cool penguin users, you will also need to install GitHub CLI as we will be working from the terminal. To install it, use the command

brew install gh

Now, the next steps are focussed on the GitHub configuration in order to be able to work without any further problems. The first thing will be to create an SSH key, which can be done with the following command. Do not forget to change the email with the one used to create your GitHub account.

ssh-keygen -t ed25519 -C "[email protected]"

You will be asked to Enter a file in which to save the key, you can leave the default one by just pressing Enter (which is what I recommend), or change it. The next prompt will ask you to Enter passphrase; citing the GitHub documentation (again):

With SSH keys, if someone gains access to your computer, the attacker can gain access to every system that uses that key. To add an extra layer of security, you can add a passphrase to your SSH key. To avoid entering the passphrase every time you connect, you can securely save your passphrase in the SSH agent.

I'm not going to cover that, you can refer to the official docu, I will proceed assuming you DID NOT Enter passphrase and just press Enter twice. In order to finish this terrible and scary part, you will add the SSH key you just generated to the ssh-agent and to your GitHub account.

Add SSH key to the ssh-agent

The first step is to start the ssh-aggent in the background with the command

eval "$(ssh-agent -s)"

If you're using macOS Sierra 10.12.2 or later (do not ask me how to know that 'cause I don't know), you will need to modify the ~/.ssh/config file to automatically load keys into the ssh-agent.

To begin with, check if the file exists with open ~/.ssh/config, if it does not, create it with the command

touch ~/.ssh/config

Now, open it and modify it to contain the following lines

Host github.com
  AddKeysToAgent yes
  UseKeychain yes
  IdentityFile ~/.ssh/id_ed25519

NOTE: If your SSH key file has a different name or path than the example code, modify the filename or path to match your current setup.

NOTE 2: If you DID NOT add a passphrase to the key, remove the UseKeychain yes line.

Finally, add the SHH key to the shh-agent with the command

ssh-add ~/.ssh/id_ed25519

NOTE: If you DID add a passphrase to the key, the command should be ssh-add --apple-use-keychain ~/.ssh/id_ed25519

Add SSH key to your GitHub account

Before adding the SSH key, you need to authenticate with the command

gh auth login

This command will lead you to an interrogation, but do not worry, I have the answers for you:

First Question: What account do you want to log into?
GitHub.com

Second Question: What is your preferred protocol for Git operations?
SSH

Third Question: Upload your SSH public key to your GitHub account?
/home/YOUR_USER_NAME/.ssh/id_ed25519.pub

Fourth Question: Title for your SSH key:
key_name

Last Question: How would you like to authenticate GitHub CLI?

• If you are a hero that has and remembers its token: Paste an authentication token

• If you are a mortal like me: Login with a web browser

And finally, you are ready to go! Or at least you should be...

Contributors

Alba Jiménez | Contact me

Diego Benito | Contact me

Ian Perez | Contact me

Iris Mestres | Contact me

Junior Contributors

Antonio Arcas | Contact me | Daisy thought that Comet was a planet.

Maria Lopez | Contact me | No loses, with each crisis I either succeed or learn.

Tassnime Reddahi | Tassnimered | "Let me infect you with some of my positive energy"

Irene Porta | IrenePorta | I'm a chill person, my mind is not.