Git commands

I will be using this very simple repository in order to have a fast access to the most used commands in git and operations in git and Git-Hub.

Adding an SSH key

On windows

GO to C:\Users\username.ssh and check that you have the id_rsa, id_rsa.pub, known_hosts and known_hosts.old, if this files are there, go to id_rsa.pub and add it into your account if it is not there. If the files do not appear or some is missing remove all the contents of the folder and start generating them. To do so open power shell and pass the following commands: ssh-keygen -o -t rsa -c "your email if wanted", do not specify any file anme and any passphrase (it is not necessary), this will create the id_rsa and the id_rsa.pub files. Add the ssh key to your account and the next time you use it (only first) when cloning for example a repo you will be asked if you want to use it, type yes and the ssh key has been enabled !
Here a guide on how to do it: https://www.youtube.com/watch?v=Irj-2tmV0JM&lc=Ugzh8-D4uZ83ENeMkwp4AaABAg

On Linux

On Linux this commands will be enough:
cd ~/.shh
ssh-keygen -t rsa -b 4096 -C "your email if wanted"
eval $(ssh-agent -s)
ssh-add "/home/username/.ssh/ssh_file_name"

Add then the add public key to your account.

Here a guide on how to do it: https://www.youtube.com/watch?v=EoLrCX1VVog&t=77s

Introducing Git into a repository.

This are the commands that we will be using in order to start a git instance in any directory and connect it with a remote repo in Git-Hub.
git init
git add .
git commit -m "first commit"
git remote add origin git@github.com:username/name_of_repo Connect the local directory to Git-Hub.
git push -u origin main Normally the main branch is the first created.

The basic commands staging your changes

git init Start a git instance, now files in the directory will be tracked.
git status Check the status of your files.
git add "name_of_files" Add the files to git so it tracks them.
git commit -m "message" Commit the changes done staged by the add command.
git push Push the changes to the remote version of the repository in Git-Hub.

Create and work with branches

git branch Get the branches of the project and locate the working branch.
git checkout -b "name_of_the_branch" Create a new branch.
git checkout "name_of_the_branch" Change the branch you are in.
git push --set-upstream origin "name_of_the_branch" Push that new branch to the remote repository.
git merge "name_of_the_branch_to_merge_in"

Special case (Change the the name of a branch)

git branch -m "new_branch_name"
git push origin -u "new_branch_name"
git push origin --delete "old_branch_name"

Get information from the remote version of the repository to our machine

git clone "repo_to_clone" Download the remote repository from Git-Hub to the local machine.
git fetch Get all the info from all the existing branches remotely.
git pull origin "name_of_the_branch" Pull a branch.
git push origin "name_of_the_branch" Push a branch.

Special case (Clone a single branch of a project)

git clone --single-branch --branch "name_of_the_branch"

ZSH-Terminal

This is an extended version of the Bourne Shell (sh) - default terminal for Linux systems - which supports the use of plug-ins and is higly personalizable. In this section I will save some useful code to use this terminal.

Install ZSH

sudo apt install zsh
sh -c $(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh) sudo chsh -s $(which zsh) To make the zsh as default terminal.

ZSH Terminal setup

Themes

We will download and install the MesloLGS NF font which can be found at the github link below.
We will also use the powerlevel10k theme to get a good and visually atractive and also useful terminal: https://github.com/romkatv/powerlevel10k.

Plug-ins

Syntax highlighting: https://github.com/zsh-users/zsh-syntax-highlighting/blob/master/INSTALL.md
Autosuggestion: https://github.com/zsh-users/zsh-autosuggestions/blob/master/INSTALL.md
You-should-use: https://github.com/MichaelAquilina/zsh-you-should-use
exa: https://github.com/ptavares/zsh-exa
ripgrep: https://github.com/BurntSushi/ripgrep?tab=readme-ov-file#installation
fzf: https://www.linode.com/docs/guides/how-to-use-fzf/

Uninstall ZSH

sudo apt-get --purge remove zsh

Anaconda

Anaconda is a python (and R) open-source which includes multiple tools that can make it quite easy to download, install and work with different bioinformatic tools. The key pro to learn anaconda is the use of different environments which enable us to work with different versions of R and Python and libraries with ease. I will put here some useful commands I normally use or that I have to use and that in some cases I tend to forget.

Anaconda environments management

conda create --name "env_name" Create an environment.
conda activate/deactivate "env_name" Activate or Deactivate an environment.
conda remove --name "env_name" --all Remove an environment.
conda env list List all the installed environments.
conda list "name_of_package" All the packages/tools installed in your.
environment, if we specify a package/tool it will show them only.

Use-case (Install STAR 8.9.3 with python3)

conda create -n star_env python=3.9
conda install -c bioconda star=8.9.3

Import and export

conda env export | grep -v "^prefix: " > environment.yml Save the environment state of the current environment.
conda env create -f environment.yml Create an environment from a .yml file.