Appendix A — System administration

A.1 System installation

Proceed as follow to install Debian (server configuration):

• Download the official Debian image at https://www.debian.org/.
• Create a bootable USB drive w/:

## Create bootable USB drive on Linux ----
dd if=debian-99.9.9-amd64.iso of=/dev/sdX bs=4M status=progress && sync

• Restart and boot from the USB drive.
• Select Graphical install and follow instructions.
• Partition disks as follow:

Storage virtualization technology	Space	Path
RAID 1	512 Mo	/boot/efi
	50 Go	swap
	396 Go	/
RAID 5	6 To	/home

• Install SSH server and Standard system utilities only.
• Restart and remove USB drive.

A.2 System configuration

Use the command su - to switch to root user (sudo utility is not installed).

A.2.1 System update

## Update system ----
apt-get update && apt-get upgrade

A.2.2 Timezone

## Set timezone ----
timedatectl set-timezone Europe/Paris

## Set automatic time synchronization ----
systemctl enable systemd-timesyncd

A.2.3 Network configuration

Use ip link to list network interfaces.

## Edit network configuration file ----
nano /etc/network/interfaces

## # This file describes the network interfaces available on your system
## # and how to activate them. For more information, see interfaces(5).
## 
## source /etc/network/interfaces.d/*
## 
## # The loopback network interface
## auto lo
## iface lo inet loopback
## 
## # The primary network interface
## auto eno1np0
## iface eno1np0 inet static
##         address 92.168.45.3                         [ ## ]
##         netmask 255.255.255.0
##         network 192.168.0.0
##         broadcast 192.168.0.255
##         gateway 192.168.0.254
##         dns-nameservers 999.99.999.99 999.99.999.99 [ ## ]

## Apply changes ----
systemctl restart networking.service

## Check network ----
ping -c 5 1.1.1.1

## Check DNS ----
ping -c 5 archlinux.org

A.2.4 APT sources

## Edit APT software repositories (add contrib & non-free sources) ----
nano /etc/apt/sources.list

## deb http://deb.debian.org/debian/ bookworm main contrib non-free non-free-firmware
## deb-src http://deb.debian.org/debian/ bookworm main contrib non-free non-free-firmware
## 
## deb http://security.debian.org/debian-security bookworm-security main non-free-firmware
## deb-src http://security.debian.org/debian-security bookworm-security main non-free-firmware
##
## # bookworm-updates, to get updates before a point release is made;
## # see https://www.debian.org/doc/manuals/debian-reference/ch02.en.html#_updates_and_backports
## deb http://deb.debian.org/debian/ bookworm-updates main non-free-firmware
## deb-src http://deb.debian.org/debian/ bookworm-updates main non-free-firmware

## Apply changes ----
apt-get update

A.2.5 Nvidia driver

## Install Nvidia utility ----
apt install nvidia-detect

## Detect graphic card ----
nvidia-detect

## Install Nvidia driver ----
apt install nvidia-driver

A.2.6 SSH server

## Configure SSH server ----
nano /etc/ssh/sshd_config

## Port 2222
## LoginGraceTime 30s
## MaxAuthTries 6
## PermitRootLogin no
## PermitEmptyPasswords no
## PubkeyAuthentication yes
## AuthorizedKeysFile .ssh/authorized_keys .ssh/authorized_keys2
## AllowGroups sshlogin

## Create new group -----
groupadd sshlogin

## Add user to <sshlogin> ----
usermod -aG sshlogin <user>

## Apply SSH server changes ----
systemctl restart ssh

A.2.7 Firewall

## Install firewall ----
apt-get install ufw

## Deny all incoming ----
ufw default deny incoming

## Accept all outgoing ----
ufw default allow outgoing

## Accept SSH protocol ----
ufw allow 2222/tcp

## Apply changes ----
ufw enable

## Check ----
ufw status

A.2.8 Reboot system

## Reboot system ----
reboot

A.3 Software installation

Use the command su - to switch to root user.

A.3.1 Install utilities

## Update APT sources ----
apt-get update

## Install utilities ----
apt-get install              \
  apt-transport-https        \   ## Secure APT transport
  build-essential            \   ## Tools for compiling software
  ca-certificates            \   ## Common CA certificates
  curl                       \   ## File download manager
  dirmngr                    \   ## Network certificate management service
  ffmpeg                     \   ## Tools for transcoding multimedia files
  figlet                     \   ## ASCII banners generator
  fontconfig                 \   ## Font configuration library 
  git                        \   ## Version control system
  gnupg                      \   ## Secure communication and data storage
  htop                       \   ## Interactive processes viewer
  imagemagick                \   ## Image manipulation program
  lsb-release                \   ## Linux release reporting utility
  ncdu                       \   ## Disk usage viewer
  neofetch                   \   ## Display system information & logo
  neovim                     \   ## Fork of Vim CLI editor
  ntfs-3g                    \   ## Support for the NTFS filesystem
  nvtop                      \   ## GPU monitoring tool
  rsync                      \   ## File-copying tool
  screen                     \   ## Terminal multiplexer
  software-properties-common \   ## Repositories manager
  tmux                       \   ## Terminal multiplexer
  tree                       \   ## Displays an indented directory tree
  vim                        \   ## CLI editor
  wget                       \   ## File download manager
  zip                        \   ## Archiver for .zip files
  zsh                            ## Shell with lots of feature

A.3.2 Install R

## Add CRAN GPG key ----
gpg --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7'
gpg --armor --export '95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7' | gpg --dearmor | tee /usr/share/keyrings/cran.gpg > /dev/null

## Add CRAN repository ----
echo "deb [signed-by=/usr/share/keyrings/cran.gpg] https://cloud.r-project.org/bin/linux/debian bookworm-cran40/" | tee /etc/apt/sources.list.d/cran.list

## Update APT sources ----
apt-get update

## Install R ----
apt-get install r-base r-base-dev

## Install Pandoc ----
apt-get install pandoc

## Install additional tools for some R packages ----
apt-get install        \
  cmake                \
  libgdal-dev          \
  libproj-dev          \
  libgeos-dev          \
  libudunits2-dev      \
  libnode-dev          \
  libcairo2-dev        \
  libnetcdf-dev        \
  libmagick++-dev      \
  libpoppler-cpp-dev   \
  libgmp3-dev          \
  libharfbuzz-dev      \
  libfribidi-dev       \
  libmpfrc++-dev       \
  libfftw3-bin         \
  libfftw3-dev         \
  libgsl-dev           \
  libssl-dev           \
  libxml2-dev          \
  libcurl4-openssl-dev

A.3.3 Install RStudio server

## Install utility ----
apt-get install gdebi-core

## Download RStudio server installer ----
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2024.04.2-764-amd64.deb

## Install RStudio server ----
gdebi rstudio-server-2024.04.2-764-amd64.deb

## Configure RStudio server ----
nano /etc/rstudio/rserver.conf

## # Server Configuration File
## www-port=8787

## Configure RStudio session ----
nano /etc/rstudio/rsession.conf

## # R Session Configuration File
## session-timeout-minutes=0

A.3.4 Install Quarto

## Download Quarto installer ----
wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.5.55/quarto-1.5.55-linux-amd64.deb

## Install Quarto ----
dpkg -i quarto-1.5.55-linux-amd64.deb

A.3.5 Install Python

## Install Python ----
apt-get install   \
  python3         \
  python3-dev     \
  python3-pip     \
  python3-venv    \
  python3-sphinx

A.3.6 Install Docker

## Download Docker GPG key ----
curl -fsSL https://download.docker.com/linux/debian/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg

## Add Docker repository ----
echo \
 "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian \
 $(. /etc/os-release && echo "$VERSION_CODENAME") stable" | \
 tee /etc/apt/sources.list.d/docker.list > /dev/null

## Update APT sources ----
apt-get update

## Install Docker ----
apt-get install docker-ce

## Add user to Docker group ----
usermod -aG docker <user>

A.3.7 Install others

## Install exiftool ----
wget https://exiftool.org/Image-ExifTool-12.90.tar.gz
gzip -dc Image-ExifTool-12.90.tar.gz | tar -xf -
cd Image-ExifTool-12.90
make install
cd .. && rm -rf Image-ExifTool-12.90
rm Image-ExifTool-12.90.tar.gz

## Install ctop ----
wget https://github.com/bcicen/ctop/releases/download/v0.7.7/ctop-0.7.7-linux-amd64 -O /usr/local/bin/ctop
chmod +x /usr/local/bin/ctop

## Install lazygit ----
LAZYGIT_VERSION=$(curl -s "https://api.github.com/repos/jesseduffield/lazygit/releases/latest" | grep -Po '"tag_name": "v\K[^"]*')
curl -Lo lazygit.tar.gz "https://github.com/jesseduffield/lazygit/releases/latest/download/lazygit_${LAZYGIT_VERSION}_Linux_x86_64.tar.gz"
tar xf lazygit.tar.gz lazygit
install lazygit /usr/local/bin
rm -rf lazygit

A.4 System administration

A.4.1 Create group

## Create new group -----
groupadd cesab

## Add user to group ----
usermod -aG cesab <user>

A.4.2 Mount disk

## Create mount point ----
mkdir /media/sancho

## Change owner ----
chown -R root:cesab /media/sancho

## Change permissions ----
chmod 770 -R /media/sancho

## Mount disk ----
mount /dev/sdX1 /media/sancho

## Get disk UUID ----
ls -l /dev/disk/by-uuid/*

## Mount disk at start up ----
nano /etc/fstab

## /dev/disk/by-uuid/cdda4997-fdbd-4dff-af35-24b46f697f03 /media/sancho ext4 defaults 0 0

## Mount all ----
mount -a

## Test fstab configuration ----
systemctl daemon-reload

A.4.3 Create user

## Define variable ----
username="jdoe"

## Create new user ----
useradd -m -G sshlogin,cesab,docker -s /bin/bash $username -p 12345678

## Reset password on first login ----
passwd -e $username

## Create external drive directory ----
mkdir -p /media/sancho/$username

## Change owner ----
chown -R $username:$username /media/sancho/$username
    
## Set permissions ----
chmod 750 -R /media/sancho/$username

A.4.4 Delete user

## Delete user from system ----
userdel -r $username

## Remove external drive directory ----
rm -rf /media/sancho/$username

A.5 Customization

A.5.1 Nerd fonts

## Install font utility ----
apt-get install fontconfig

## Create fonts/ directory ----
mkdir -p /usr/share/fonts/truetype/
cd /usr/share/fonts/truetype/

## Get latest release of NF GitHub repo ----
NF_VERSION=$(curl -s "https://api.github.com/repos/ryanoasis/nerd-fonts/releases/latest" | grep -Po '"tag_name": "\K[^"]*')

## Download Nerd Fonts ----
wget https://github.com/ryanoasis/nerd-fonts/releases/download/${NF_VERSION}/FiraCode.zip
wget https://github.com/ryanoasis/nerd-fonts/releases/download/${NF_VERSION}/Hack.zip
wget https://github.com/ryanoasis/nerd-fonts/releases/download/${NF_VERSION}/Meslo.zip

## Extract ZIP content ----
unzip FiraCode.zip -d FiraCode && rm FiraCode.zip
unzip Hack.zip -d Hack && rm Hack.zip
unzip Meslo.zip -d Meslo && rm Meslo.zip

## Install fonts ----
fc-cache -f -v

A.5.2 ZSH and plugins

## Change ZSH dotfile location ----
nano /etc/zsh/zshenv

## ZDOTDIR=$HOME/.config/zsh

## Create zsh directories ----
mkdir -p ~/.cache/zsh
mkdir -p ~/.config/zsh

## Define ZSH as default shell ----
chsh -s /usr/bin/zsh root

## Download Oh My ZSH installer ----
wget https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh

## Install Oh My ZSH ----
ZSH="$HOME/.config/oh-my-zsh" sh install.sh

## Remove Oh My ZSH installer ----
rm install.sh

## Install prompt theme ----
ZSH_CUSTOM=$HOME/.config/oh-my-zsh

git clone https://github.com/romkatv/powerlevel10k.git             ${ZSH_CUSTOM}/themes/powerlevel10k

## Install ZSH plugins ----
git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUSTOM}/plugins/zsh-syntax-highlighting

git clone https://github.com/zsh-users/zsh-autosuggestions.git     ${ZSH_CUSTOM}/plugins/zsh-autosuggestions

## Edit ZSH configuration file ----
nano ~/.config/zsh/.zshrc

## # Path to your Oh My Zsh installation.
## export ZSH="$HOME/.config/oh-my-zsh"

## # History
## HISTFILE=$HOME/.cache/zsh/history

## # Prompt Theme
## ZSH_THEME="powerlevel10k/powerlevel10k"

## # ZSH plugins
## plugins=(git zsh-autosuggestions zsh-syntax-highlighting z)

## # Aliases
## alias ..='cd ..'
## alias ls='ls --color=auto'
## alias ll='ls --color=auto -al'
## alias r="R"
## alias gs='git status'
## alias ga='git add'
## alias gc='git commit -m'
## alias gp='git push'

## # Hotkeys
## bindkey '[C' forward-word
## bindkey '[D' backward-word

## Apply changes ----
source ~/.config/zsh/.zshrc

A.5.3 MOTD

## Move to MOTD config directory ----
cd /etc/update-motd.d

## Remove content ----
rm -rf ./*

## Define colorscheme ----
nano colors

## NONE="\033[m"
## WHITE="\033[1;37m"
## GREEN="\033[1;32m"
## RED="\033[0;32;31m"
## YELLOW="\033[1;33m"
## BLUE="\033[34m"
## CYAN="\033[36m"
## LIGHT_GREEN="\033[1;32m"
## LIGHT_RED="\033[1;31m"

## Print hostname (Figlet) ----
nano 00-hostname

## #!/bin/sh
## 
## . /etc/update-motd.d/colors
## 
## printf "\n"$LIGHT_RED
## figlet "  "$(hostname -s)
## printf $NONE
## printf "\n"

## Print system info (Neofetch) ----
nano 10-banner

## #!/bin/bash
## 
## echo ""
## neofetch --config /home/ncasajus/.config/neofetch/config.conf
## 
## echo "Welcome to Rossinante  !"
## echo ""

## Remove previous MOTD ----
rm /etc/motd

## Apply changes ----
ln -s /var/run/motd /etc/motd

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