2  Install core software on Ubuntu

2.1 Ubuntu general guidelines

2.1.2 Ubuntu file, and package structure

2.1.2.1 System-wide location (for core programs)

System-wide affects all users, are installed using sudo, on the root of the system.

Location Purpose
/usr/bin System executables (APT)
/etc System-wide configuration (example: define repositories for apt)
/opt Vendor (external) apps
/usr/local/bin Admin-installed software
/var Logs, caches, databases
Table 2.1: Main system-wide software locations
  • /opt for third-party application bundles, self-contained while /usr/local is for third-party binaries. Besides, /opt is not in the path by default.

2.1.2.2 User-specific locations

User does not require root

Location Purpose
~/Applications AppImages
~/.local/bin User executables
~/scripts/tools Custom bash executables
~/.local/share User app data, notably ~/.local/share/applications storing desktop icons
~/.config User configuration
Table 2.2: Main user-based software locations, to be compared with Table 2.1

Detailed structure of Ubuntu package layout

Detailed structure of Ubuntu package layout

  • usr folder stores read-only executables, while /var is regularly written upon changes:

    • /var/lib: apt and dpkg databases, for instance, respectively stored under dpkg, and /apt
    • /var/cache: metadata caches for faster execution

  • /usr/local/, or $HOME/.local stores executables that require custom compilation with make, or qmake, rendered from manual archives:

    • bin, sbin for executables
    • share for icons (under subfolder icons) and desktop configuration, document ion under /doc
    • lib for extensions of a given executable (such as packages in R, or modules in Python)
    • This folder hierarchy follows XGDBase Directory Npecification

  • /tmp for temporary folders, cleaned after reboot

  • /run for sockets, namely used for controlling all the protocols running in the background for connecting to a server, such as the ssh-agent

  • ~/.config/systemd: lists all processes that keep on running in the background, such as Cursor updates, or One drive synchronisations.

2.1.4 Monitor processes running in the background, and on startup

  • systemctl list-unit-files --type=service --state=running --user to list all processes running in the background, even after rebooting, restrained to the user-level.
    • Alternatively, processes at the system-level are stored under /lib/systemd/system/
  • systemctl status <service> retrieves current status

2.1.5 Network protocols, and connexion troubleshoots

  • Two IP protocols for Wi-FI: IPv4 versus IPv6.

    TipThe two Internet protocols, namely IPv4 vs IPv6

    IPv4 is older, but still prevailing in many websites, such as Github, or OneDrive:

    • Uses 32-bit addresses (e.g. 192.168.1.10)
    • Used by most websites, CDNs, VPNs, corporate services
    • But the 32-limitation hinders the number of avalaible IP addresses.

    IPv6 is newer, but not universally supported:

    • Uses 128-bit addresses (e.g. 2a01:cb14:86a7::1)
    • Supported by modern ISPs and operating systems
    • Some networks provide IPv6-only, with no IPv4 fallback. Espaically the case with Microsoft services, governmental or academic websites.

  • You can test if this is the issue to connect to some websites with curl <webdomain>, such as curl https://onedrive.live.com, returning Cannot connect

  • Recent modern routers return only IPv6 -> while Windows is able to able to auto-fall back to IPv4, this is not the case of IPv6.

    • Temporary fix: by running the following instructions, you solve this issue by automatically configuring a IPv4 upon failure. Recommended only for short-term debugging.
    install dhclient commands
sudo dhclient -4 wlp2s0f0 <Wifi-name> ## in my case, wlp2s0f0

    • Permanent fix2:

      nmcli connection modify "Routeur/Livebox-FC77" ipv4.method auto 
nmcli connection modify "Routeur/Livebox-FC77" ipv6.method auto ## connect automatically to IPv4 or IPv6, depending on the availitbity of the protocol
## re-start the connection, applying the new configuration parameters
nmcli connection down "Routeur/Livebox-FC77"
nmcli connection up "Routeur/Livebox-FC77"

2.1.5.1 Eduroam connexion

  1. Ensure to delete beforehand any pre-existing installation: rm -rf $HOME/.config/cat_installer.
  2. Go to https://cat.eduroam.org/, the website usually provides with the version fitting your OS distribution.
  3. On Linux, download the Python script, choosing AMU university.
  4. Run Python script with python 3 eduroam-linux-AUA.py
  5. As userid, provide your academic mail address, and as password, your ENT password.

2.1.6 Pimp your shell: switch from boring Bash to fancy Zsh

  1. Installation script:
sudo apt update
sudo apt install zsh

## change the default shell shebang
chsh -s $(which zsh) ## modify /etc/passwd repository
reboot # required log out for effective changes

## check if zsh is used by default (also the theme is modifed)
getent passwd "$USER" -> return "/home/bastien:/usr/bin/zsh"

## Install advanced customisation of the shell with Install Oh My Zsh addon
sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)" # create automatically the ~/.zshrc configuration file

You should keep the original ~/.bashrc as a fallback for Bash.

  1. Install the modern alternative to ls, namely eza
# install the gpg command
sudo apt update
sudo apt install -y gpg

# install eza
wget -qO- https://raw.githubusercontent.com/eza-community/eza/main/deb.asc | sudo gpg --dearmor -o /etc/apt/keyrings/gierens.gpg
echo "deb [signed-by=/etc/apt/keyrings/gierens.gpg] http://deb.gierens.de stable main" | sudo tee /etc/apt/sources.list.d/gierens.list
sudo chmod 644 /etc/apt/keyrings/gierens.gpg /etc/apt/sources.list.d/gierens.list
sudo apt update
sudo apt install -y eza
  1. Change the behaviour of the shell:

  • System-wide: all exe installed under /usr folder can be called directly from the $PATH. For third-party apps stored under /opt, you must add a symlink redirecting to your local folder: sudo ln -s /opt/<appName> /usr/local/bin/<appName>.

  • User-level: customise .bashrc (and .zshrc if using the .zshfancy shebang) -> Only affects the current user, see my own .zshrc configuration file, and below lsoutput Figure 2.1.

Modified bahaviour of the ls output

Modified bahaviour of the ll output, displaying addition to file names their sizes, permission rights, and original proprietary

The la output displays in addition to the lloutput the hidden files (traitdionally starting with a .)

The lt output is combination of both lsand treeto display the hierarchical structure of a folder
Figure 2.1: Visual representation of my customised lscommands to display the content of a folder from a Bash terminal.

Useful resources:

2.2 Synchronise files across devices with OneDrive

2.2.1 OneDrive open-source installation for Ubuntu

  1. Install dependencies:
sudo apt install build-essential libcurl4-openssl-dev pkg-config git -y
  1. Add the OpenSuSE Build Service repository release key
wget -qO - https://download.opensuse.org/repositories/home:/npreining:/debian-ubuntu-onedrive/xUbuntu_24.04/Release.key | gpg --dearmor | sudo tee /usr/share/keyrings/obs-onedrive.gpg > /dev/null

echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/obs-onedrive.gpg] https://download.opensuse.org/repositories/home:/npreining:/debian-ubuntu-onedrive/xUbuntu_24.04/ ./" | sudo tee /etc/apt/sources.list.d/onedrive.list

## update cache
sudo apt-get update
  1. Install OneDrive:
sudo apt install --no-install-recommends --no-install-suggests onedrive
  1. Sync OneDrive:

  1. Exclude large folders, and directories that are complex and are not recommended for syncing, nano ~/.config/onedrive/config. You can see the actual content of my config file under onedrive-custom-config.3

  2. Authenticate, and run OneDrive once

onedrive --sync --dry-run ## optional, list folders that will be synchronsied
onedrive --sync --verbose ## first initialisation, usually time-consuming, one-shot
  1. Permanent synchronization using systemtcl facilities. Choose either this approach, or the visual approach detailed in Tip 2.1, as they can’t operate simultaneously.
systemctl --user enable onedrive
systemctl --user start onedrive ## in the back end, use onedrive --monitor
  1. Monitor currently uploaded files:
journalctl --user-unit onedrive -f (continous) ## equivalent to systemctl --user status onedrive (single-shot)

onedrive --display-config
onedrive --version
  1. Other useful OneDrive instructions:
  • onedrive --create-share-link <path/to/file> for read-only shareable links, and onedrive --create-share-link <path/to/file> --with-editing-perms to add writing rights.
Tip 2.1: GUIs for OneDrive monitoring

OneDrive system tray program adds a simple icon returning the status of synchronization for OneDrive.

Installation bash:


## install the 5th version of qmake
sudo apt install qt5-qmake qtbase5-dev

## create the runnable executive file
git clone https://github.com/DanielBorgesOliveira/onedrive_tray.git
cd onedrive_tray
mkdir build
cd build
/usr/lib/qt5/bin/qmake ../systray.pro ## prepare the configuration, such as Makefile
make ## build the software

## execute it, such that it runs whenever log in
sudo make install ## deploy the software, such as copying files -> here's the sudo incentive
systemctl enable --user onedrive_tray.service

Colour the logs output reported on the terminal:

  1. Install dependencies: sudo apt install silversearcher-ag ccze
  2. Add onedrive_log bash file into folder ~/scripts/tools.
  3. Add permanently to the $PATH by modifying the ~/.bashrc file: export PATH="$PATH:$HOME/scripts/tools"/

2.2.2 Troubleshoots for OneDrive

  • Call systemctl --user restart onedrive after modifying the .config file to account for changes within it. For retro-application of configuration changes, use onedrive --resync --sync --verbose with parsimony. The synchronisation halts without warning, when the config file is modified, so you need to restart it.

  • Warning β€œonedrive application is already running, please check process list” means that several concurrent onedrive are running in the background:

    • List existing processes using onedrive: ps aux | grep onedrive
    • Force kill processes that do no not use systemtcl: kill -9
    • \(90\%\) of the time is that you’re simultaneously running UI OneDrive, and in the background systemtcl for synchronising processes

Git and OneDrive do not combine well for:

  • Different encoding of end of line: Linux (and Mac) machines end lines with LF (Line Feed): \n, while Windows uses CRLF (Carriage Return + Lien Feed): \r\n
  • Linux tracks file permissions for executables while Windows doesn’t (only problematic for shell scripts)
  • .git and .Rproj folders are complex binary repositories often OS dependent.

To avoid these issues:

  1. Configure globally the .gitconfig configuration file to allow both end of lines indicators, using git config --global core.autocrlf input on Linux and Mac machines collaborating with Windows machines4, and git config --global core.autocrlf true on Windows machines5.

  2. For further robustness, create a .gitattributes dotfile per project6:

## 3 columns: file extension, file type (text, or binary), eol definition for text documents
*.sh   text eol=lf
*.py   text eol=lf
*.js   text eol=lf
*.ts   text eol=lf
*.java text eol=lf
Then, apply the changes with the following Git commands^[this command first identifies all files tracked by Git, then apply to every file the end of line normalisation rule, with `.gitattributes` prevailing over the global `core.autocrlf` option]
git add --renormalize .
git status ## display files being impacted by the change of EOL encoding
git commit -m "Normalize line endings"
  1. Configure the editor default end of line encoding:
  • VS Code: , then type β€œOpen VS Code Settings”, then go to β€œFiles:EOL”, and set end of line as \n
  • RStudio: Tools β†’ Global Options β†’ Code β†’ Saving -> Line ending Conversion β†’ (Posix) LF.

Best practices for End of Line homogenisation across devices

Best practices for End of Line homogenisation across devices
WarningGraphical Interfaces for OneDrive

Avoid using graphical interfaces, such as OneDriveGUI, they poorly concur with local installation of onedrive on my personal experiment.

Instead, rely on the terminal, as it usually provides the user with better customisation, and control on OneDrive configuration.

Many modern editors, such as LibreOffice and Rstudio use atomic save strategies to preserve data integrity when writing files.

file.qmd
↓ edit
file.qmd.tmp ## If OneDrive synchronises in the meantime, it believes that the file had been discarded
↓ rename
file.qmd


## Architecture causing this problem
RStudio
   β”‚
   β”‚ save
   β–Ό
Local file (.qmd)
   β”‚
   β”‚ filesystem event
   β–Ό
onedrive client
   β”‚
   β”‚ sync
   β–Ό
OneDrive cloud
   β”‚
   β”‚ sync back
   β–Ό
local overwrite

This process is likely to interfere with the regular synchronisation protocol of the onedrive client relying on inotify, triggering editor warnings, or even temporary removal of files contents.

Three complementary solutions to address these issues, and reduce conflicts between editor saves and sync detection.

  1. Do not put active projects inside OneDrive, setting apart large documents storage synchronised with OneDrive, from source code version by Git.
  2. Pause sync while coding. But you need to think about restarting the synchronisation afterwards.
  3. Twist the configuration file, helping with editors using atomic saves:
force_session_upload = "true" ## avoid overwriting by older cloud versions, when RStudio is on its way of saving
delay_inotify_processing = "true" ## wait for RStudio to finalise the saving of tmp files before synchronising to OneDrive

2.3 Software to install

**General recommendation*: avoid using ChatGPT, as the instructions for installing software are often deprecated and/or not following Ubuntu best guidelines.

Three recommended methods, depending on Ubuntu’s support:

  1. If supported by Ubuntu, go for apt install for system software7:

  • automatic updates and security patches -> it’s the only method allowing it in a systematic way.

  • easiest method for installation

  • signed and verified packages

  • recommended for core system, long-term software

  • If not directly available on Ubuntu’s native package manager, or using in the back-end snap commands, switch to pre-built tarball installation8, or add the repository (only if trusted) to apt allowed keys folder. Example for Docker, Section 2.3.6, or custom Zotero installation file.

  • .deb files are intended for Linux distributions derived from Debian (such as Ubuntu, Linux Mint, etc.), while .rpm files are mainly used by distributions derived from Red Hat–based systems (such as Fedora, CentOS, and RHEL) + openSUSE distribution:

    • No auto-updates
    • Potential dependency issues
    • Always install with sudo apt install, rather than sudo dpkg -i, to better solve dependencies, fix broken installs, and ensures system consistency.
  1. AppImages are standalone executable files, bundling the application and most of its dependencies:
  • Recommended for desktop applications to be installed only on the user account -> does not require sudo rights in most cases
  • Portable
  • AppImageLauncher can help in organising all AppImages within the same folder + integrate them into the system menus:
    • Relevant if using multiple AppImages
    • Avoid Snap
  1. Pre-built tarball (.tar(gz|xz)) archives:
  • Stronger customisation
  • Works without distribution packages
  • Requires manual handling/no automatic updates
  • Only recommended for developers, or if nothing else exists.
  • And now, the least recommended installations:
    • snap stores pre-compiled versions of tools, but are less recommended compared to standard installation with sudo apt install
    • FlatPak+Flathub

Guidelines for installing software on Ubuntu

Guidelines for installing software on Ubuntu

portable, or not. Portable installation is easier to remove, as it does not leave leftovers in the core system, but does not allow for automatic updates. On the other hand, non-portable applications are usually better for daily/intensive use, but not sandboxed, and harder to remove.

2.3.1 Git and GitHub configuration

  1. Github often requires double authentication, that you can set on https://github.com/settings/security. Recommended to use passkey if supported by your device (unfortunately, Linux OS usually do not support it), or use authenticator app, such as Microsoft Authentificator. Deterred against the use of SMS + mobile phones.

  2. Configure your access to Github:

  1. Choose either SSH, or HTTPs.
  2. For HTTPS, configure one token per device, under https://github.com/settings/tokens. Give the token the name of your laptop, its configuration and originals owner. Assign it at least the repo and read scopes. Copy it once -> it won’t be available afterwards!!.
  1. General options to configure:
  1. Use either the command line (create also automatically the file ~/.gitconfig):
git config --global user.name "bastienchassagnol"
git config --global user.email "bastien.chassagnol@univ-amu.fr"
  1. Or directly, using text editor, file ~/.gitconfig (more error-prone to indentation errors). Find my default git config file here (for comprehensive description of options, report to Formation Git 2024, a tutorial by Benjamin):
[user]
  name = bastienchassagnol
  email = bastien.chassagnol@univ-amu.fr
## modern default git options
[init]
  defaultBranch = main

## simplifying solving git conflicts + troubleshoot solving
[merge]
  conflictstyle = zdiff3
[rerere]
  enabled = true

## tolerate distinct end of lines  
[core]
  autocrlf = input

## visualisation
[tag]
  sort = version:refname
[branch]
  sort = -committerdate
[credential]
  helper = store
  1. Avoid typing your password for every login:
  1. For HTTPS + PAT token protocol, use git config --global credential.helper store for permanent registration of the password (should we not encrypt the file??), or git config --global credential.helper 'cache --timeout=3600' for temporary access9.
  2. Define SSH key.

2.3.2 AppImageLauncher


## download the .deb archive, with the proper architecture configuration
## https://github.com/TheAssassin/AppImageLauncher/releases/tag/v3.0.0-beta-3
 
sudo apt install appimagelauncher_3.0.0-beta-2-gha287.96cb937_amd64.deb  

## update dependencies
sudo apt update
sudo apt install -f
  • For deleting apps installed with AppImage Launcher, you’ll need to delete both Applications folder, and ~/.local/share/applications/ that stores executables.

2.3.3 PDF management

2.3.3.1 Sioyek as PDF Viewer

Sioyek is an open-source PDF viewer focusing on technical papers with mathematical formulas. Major uses cases are coloured highlights of text sections with h shortcut, smart jump to figures by clicking on them, and bookmark text sections with shortcut b.

  1. Choose between portable (for isolated environment), or standard distribution under Sioyek releases
  2. Unzip the archive, within it, make it executable with chmod +x.
  3. Run it

To turn any exec into a desktop application on Ubuntu-GNOME, follow this steps:

  1. Relocate everything under /opt/sioyek10. **Note that the structure of a package may not follow exactly this of sioyek!!
## create required folders

sudo mkdir -p /opt/sioyek
sudo mkdir -p /etc/sioyek
sudo mkdir -p /usr/share/sioyek

## relocate, if not already done, the sioyek builds

### core executables
sudo cp ~/sioyek/build/sioyek /opt/sioyek/
sudo chmod +x /opt/sioyek/sioyek

### confgiuration files
sudo cp ~/sioyek/build/prefs.config /etc/sioyek/
sudo cp ~/sioyek/build/keys.config  /etc/sioyek/
sudo cp -r ~/sioyek/build/shaders /usr/share/sioyek/
sudo cp ~/sioyek/build/tutorial.pdf /usr/share/sioyek/
  1. Add a distinctive icon, and customise the native Ubuntu launcher β€˜Gnome’
sudo mkdir -p /usr/share/icons/hicolor/256x256/apps ## folder to store the siokey.png, downloaded from the web

sudo tee /usr/share/applications/sioyek.desktop > /dev/null <<'EOF'
[Desktop Entry]
Version=1.0
Type=Application
Name=Sioyek
GenericName=PDF Viewer
Comment=Fast keyboard-driven PDF viewer
Exec=/opt/sioyek/sioyek %path to the sioyek exe
Icon=sioyek
Terminal=false
Categories=Office;Viewer;
MimeType=application/pdf;
StartupNotify=true
EOF

## Refresh desktop database
sudo update-desktop-database

  1. (Optional) Make Sioyek the default PDF viewer, using either:

    1. GUI method:
      1. Right-click any PDF
      2. Properties β†’ Open With
      3. Select Sioyek
      4. Click Set as default
    2. or the command line:
    xdg-mime default sioyek.desktop application/pdf

## to check default
xdg-mime query default application/pdf

  2. add to the Path, creating a symbolic link

sudo ln -s /opt/sioyek/sioyek /usr/local/bin/sioyek

2.3.3.2 Sejda for editing PDFs in an interactive way

2.3.3.3 PDFtk

  • To edit PDFs, if you prefer the command line.

2.3.4 Image Editors (to replace Paint on Windows)

Sorted from closest experience to Paint, to most generalist:

  1. Drawing
  1. Add Drawing to the apt repository of allowed PPAs: sudo add-apt-repository ppa:cartes/drawing
  2. Install running sudo apt install drawing
  1. Libre Office Draw
  2. Gimp (closer equivalent to Photoshop):
sudo apt install gimp
sudo apt install gimp-plugin-registry ## add extensions
  1. Inkscape for generating vectorial, and fully deformable icons
sudo apt update
sudo apt install inkscape

2.3.5 LibreOffice

  1. Install main software (such as Libre Office Write, or Calc) with sudo apt install libreoffice libreoffice-gtk3

  2. Relevant extensions, that you can add using Tools -> Extensions

  1. Rotate Images in free text documents with Rotate extension
  2. Install dictionaries + extension Grammalecte and LanguageTool11. needs to check if LanguageTool is truly relevant, is AI-based, but also resource-consuming.
## French dictionary
sudo apt update
sudo apt install libreoffice-l10n-fr ## add French hyphenation
  1. Install Latex extension
  1. Fonts customisation:
  1. Install core Windows fonts:
sudo apt update
sudo apt install ttf-mscorefonts-installer ## Install Microsoft core fonts
fc-cache -f -v ## rebuild font cache, such that the fonts now appear In Libre Office
  1. Extra fonts installation12. Most popular fonts can be found under Every-Font GH repository:
mkdir -p ~/.local/share/fonts ## ensure personal fonts folder is created
wget -P ~/.local/share/fonts "https://raw.githubusercontent.com/serendipious/every-font/master/CenturyGothic-Italic%20-%20Century%20Gothic%20-%20Italic.ttf" ## download the original TFF files
fc-cache -f -v ## update font cache

The main stylistic variants of fonts you can play with are:

  1. Weight (Light, Regular, Bold, …)
  2. Angle or shape of the letters (regular versus italic)
  3. Width
  4. Serif vs Sans-Serif. This property is structural to a font, for instance, Times New Romanis Serif, and
    Century Gothic is Sans-serif. For data visualizations, or presentations, Sans-serif typefaces are favoured, while it’s the reverse for printed documents.
  5. Advanced font options and customisations, such as controlling for ligatures connecting two letters, can be accessed in LibreOffice β†’ Format β†’ Character β†’ Features (see Figure 2.2):

Make sure, if avalaible, to download for each font, the regular, bold, italic-bold, and italic versions at the very least.

Figure 2.2: Main typographic options

2.3.6 Docker

  1. Download dependencies, configuration files and add repository to apt for automatic updates:

sudo apt update
sudo apt install ca-certificates curl ## dependencies for downloading packages, and verifying HTTPS protocols

## Part I: create, download and make Docker apt key readable for verifying its integrity
sudo install -m 0755 -d /etc/apt/keyrings
sudo curl -fsSL https://download.docker.com/linux/ubuntu/gpg -o /etc/apt/keyrings/docker.asc
sudo chmod a+r /etc/apt/keyrings/docker.asc

## Part II: define where, and which version of Docker, should be donwloaded + how to verify its integrity
sudo tee /etc/apt/sources.list.d/docker.sources <<EOF
Types: deb
URIs: https://download.docker.com/linux/ubuntu
Suites: $(. /etc/os-release && echo "${UBUNTU_CODENAME:-$VERSION_CODENAME}")
Components: stable
Signed-By: /etc/apt/keyrings/docker.asc ## folder previously defined
EOF

## Part III: update with newer configuration
sudo apt update

  1. Install Docker toolkit with sudo apt install docker-ce docker-ce-cli containerd.io docker-buildx-plugin docker-compose-plugin

  2. Run Docker without sudorights for the main laptop user:

# create a Unix group allowing Docker to interact with system-level resources without admin rights
sudo groupadd docker
# and add curent user of the session to it
sudo usermod -aG docker $USER
  1. Check installation with sudo docker run hello-world. If not running by default upon login, enable automated start with sudo systemctl start docker. More details here.

Tutorials for Docker

2.3.7 Teams

  • Use the web version, as Microsoft no longer supports .deb versions for Linux.

2.3.8 Web browsers

2.3.8.1 Firefox

Avoid running directly sudo apt install firefox -> it installs by default snapd, and will use not stable, beta Snap version of Firefox.

  1. Import, and add Mozilla APT signing key:
## Download APT key
wget -q https://packages.mozilla.org/apt/repo-signing-key.gpg -O- | sudo tee /etc/apt/keyrings/packages.mozilla.org.asc > /dev/null

## Add it to the Apt registry
cat <<EOF | sudo tee /etc/apt/sources.list.d/mozilla.sources
Types: deb
URIs: https://packages.mozilla.org/apt
Suites: mozilla
Components: main
Signed-By: /etc/apt/keyrings/packages.mozilla.org.asc
EOF

## Provide higher priority to Mozilla Firefox

echo '
Package: *
Pin: origin packages.mozilla.org
Pin-Priority: 1000
' | sudo tee /etc/apt/preferences.d/mozilla
  1. Install Firefox using Mozilla provider:
sudo apt update
sudo apt install firefox

which firefox ## should not report `snapd` folder
apt policy firefox

2.3.8.2 Google Chrome

  1. Install Google Chrome, by downloading the .deb archive, then run it:
sudo apt install google-chrome-stable_current_amd64.deb`
  1. Download, and add Google Chrome APT signing key, for automatic updates:
## Download APT key
wget -q -O - https://dl.google.com/linux/linux_signing_key.pub | sudo gpg --dearmor -o /usr/share/keyrings/google-linux-signing-key.gpg

## Add it to the Apt registry
echo "deb [arch=amd64 signed-by=/usr/share/keyrings/google-linux-signing-key.gpg] http://dl.google.com/linux/chrome/deb/ stable main" | sudo tee /etc/apt/sources.list.d/google-chrome.list

## Update to the most recent version
sudo apt update
  1. add the Grammarly Chrome plug-in extension for automatic checking of the spelling, and grammar (choose one specific regional English, and stick to it)

2.3.9 Slack

  1. Download Slack application
  2. Run it with sudo apt install slack-desktop-4.47.69-amd64.deb
  3. Update with:

sudo apt-get update
sudo apt-get upgrade slack-desktop

2.3.10 Zulip

  1. Run following instructions:

sudo apt install curl ## if not already installed
sudo curl -fL -o /etc/apt/trusted.gpg.d/zulip-desktop.asc \
    https://download.zulip.com/desktop/apt/zulip-desktop.asc
echo "deb https://download.zulip.com/desktop/apt stable main" | \
    sudo tee /etc/apt/sources.list.d/zulip-desktop.list
sudo apt update
sudo apt install zulip
  1. Log-in (recommended with your Github profile) on each of the channels you want to connect, to keep notified about newest posts.

2.3.11 Cytoscape

Major default: only supported by Java version 17 (and not by more recent, and stable Java versions!!)

  1. Install Java version 17 with sudo apt install openjdk-17-jdk13
  2. Follow this tutorial
  1. Retrieve the latest version
  2. Make it executable with chmod u+x <filename.sh>
  3. Run with bash <filename.sh>
  4. Launch with Cytoscape &.

2.3.12 Zotero

  1. sudo apt install libreoffice-java-common -y adds Java dependencies to seamlessly integrate Zotero with Libre Office plug-in (for instance, automated retrieval of bibliographic references).

  2. Retrieve the latest stable version on https://www.zotero.org/download/14.

  3. Run following instructions + Synchronise by installing Zotero Connector on your website:


#!/bin/bash

## part I: extract archive
sudo tar -xjf zotero.tar.bz2 -C /opt
sudo mv /opt/Zotero_linux-x86_64 /opt/zotero

## Part II: add the executable
sudo ln -s /opt/zotero/zotero /usr/local/bin/zotero
  1. (Optional: add a custom Desktop, and launcher icon for an executable) Create file ~/.local/share/applications/zotero.desktop, with the following content. Make the launcher executable with chmod +x ~/.local/share/applications/zotero.desktop
[Desktop Entry]
Name=Zotero
Exec=/usr/local/bin/zotero
Icon=/opt/zotero/icons/icon128.png
StartupWMClass=Zotero
Type=Application
Terminal=false
Categories=Office;
MimeType=text/plain;x-scheme-handler/zotero;application/x-research-info-systems;text/x-research-info-systems;text/ris;application/x-endnote-refer;application/x-inst-for-Scientific-info;application/mods+xml;application/rdf+xml;application/x-bibtex;text/x-bibtex;application/marc;application/vnd.citationstyles.style+xml
X-GNOME-SingleWindow=true
  1. Inspired from Zotero hacks tutorial, enable unlimited synced storage for articles on multiple machines.
  1. Add required plug-ins, Better BibTeX (mandatory for custom expert as a plain .bib file) + Zotmoov, which replaces previous extension Zotfile for classifying articles per author’s name.
  2. Edit Zotero preferences15: - Uncheck the option to create automatic web page snapshots (increases cluttering with lots of small files added) - Uncheck full-text sync - Set apart in Edit->Settings->Advanced the
    • Base directory (should be the folder synced by your File sharing software), with
    • Custom Data directory location. This local folder should be located in a different position, and will be managed by Zotero itself
![Zotero Database Configuration](zotero-advanced-configuration.png)
  1. Edit Better BixTex plug-in: - Personally, use [auth:lower][year][journal:lower:abbr] - Should be the same across machines.

2.3.13 Quarto, R and RStudio

2.3.13.2 RStudio (Desktop IDE)

  1. Go to: https://www.rstudio.com/products/rstudio/download/#download/ Choose the Ubuntu/Debian .deb package for your architecture (amd64).
  2. Install the .deb package:
sudo apt install ./rstudio-2025.09.0-422-amd64.deb
  1. Install Air, as the recommended, fast and modern formatter for R code. Then, customise your RStudio settings, explicitly reporting the path location of Air formatter, see Tip 2.2.
uv tool install air-formatter
Tip 2.2: Sync RStudio options across platforms
  1. Locate the repository on your system that stores RStudio settings. There’s no direct means for exporting RStudio parameters that have been modified by the user. Instead, the key directory storing core RStudio settings is located under ~/.config/rstudio/ for Linux, and %AppData%\RStudio for Windows16. The key files in this repository are:
File Purpose
rstudio-prefs.json Global preferences modified by the user
keybindings/ Custom keyboard shortcuts
themes/ Custom themes (if any)
snippets/ Code snippets
dictionaries/ Custom dictionaries beyond English, and French

  1. Identify what it’s worth relevant for syncing: indeed, while you could export all the RStudio settings for a complete backup, most of them are optional, or barely modified by regular users. Instead, I would identify, and retrieve only the settings explicitly changed by the user. > Would use local, or online diff editors, such as diffcheckers to quickly identify what changed between personal configurations. > Specifically, all external tools that complement the functionalities of RStudio, such as pdf previewer, or external formatters such as Air, are hard-coded as absolute paths, and are accordingly highly specific to a personal laptop.

  2. Homogenise settings across machines: once you’ve finalised the customisation of the RStudio settings to your specific OS configuration, simply overwrite pre-existing user-specific settings file rstudio-prefs.json. Restart RStudio to check if changes were properly integrated into the graphical interface17.

To simplify the syncing across machines (especially for teams with shared computing environment), use either: 1. Git-based sync, storing your dotfiles. This is the recommended approach. You can find my settings files under rstudio-prefs.json. See also Figure 2.3 for a more comprehensive explantion of core changes brought to a default, native RStudio configuration. 2. use symbolic links, or cloud sync (but you have fewer options to adjust for changes)

In yellow, core reproducibility options. Notably, avoid loading your R session, and objects on start, for reduced use of memory

Styling and linting of R code with Air Posit, and integration with AI helpers.
Figure 2.3: Core options to change the default behaviour of RStudio, enabling enhanced compatibility across projects, R Versions, and OS platforms.

Controversial claim: use VScode for R development if working inside a Docker container, or on a server that does not provide a RStudio interface, otherwise, it’s overkilled. Notably, for R package development, that should be containerised, RStudio is way more flexible

2.3.13.3 Quarto

Go to https://quarto.org/docs/get-started/

sudo apt install ./quarto-1.3.496-linux-amd64.deb
quarto check

\[ a = 10 \]

2.3.13.4 Cursor with R

  1. Install the following R packages:
install.packages("remotes")
library(languageserver)
library(rmarkdown)
library(vscDebugger)
library(httpgd)

  1. (optional, but recommended) Use radianas enhanced R terminal with uv tool install radian

  2. Install the vscDebugger extension for VS Code, and run the debug demo script to test it.

Side by side comparison of the debug demo script, and the debugger in action

Side by side comparison of the debug demo script, and the debugger in action

2.3.14 Python

From PEP 668. guidelines, applied to modern Debian/Ubuntu distributions with native Python installed above the 3.11/3.12 version, pip is prevented from modifying the system Python as it could interfere with te core installation program apt.

This section is certainly the most controversial of this whole Ubuntu tutorial, as guidelines for a modern programmatic use of Python evolve rapidly, without reaching a full agreement

2.3.14.1 Python tools

TipModern Python development guidelines
  1. The latest versions of Ubuntu, including Noble, strongly deter from installing system-wide versions of recent Python packages. In other words, avoid running sudo apt install python3.14-full, and updating Deadsnakes PPA.
  2. uv fully replaces the functionalities and features brought by a variety of slower, standalone Python tools (pip, poetry, virtualenv, pipx, …), providing a faster, versatile and unified framework, see Figure 2.5. The features provided by poetry for package development may still not be fully covered by uv, and pipremains the legacy solution in older HPC systems:
/usr/bin ### Pre-installed Ubuntu system
 └── system Python (used by OS)

uv
 β”œβ”€β”€ managed Python versions
 β”œβ”€β”€ CLI tools (black, ruff, jupyterlab)
 └── project environments

~/.local/share/uv/python/
   β”œβ”€β”€ python3.14
  1. conda, and even mamba have been outdated by pixi for multi-language projects. uv is definitely the go-to solution for Python-centric projects, but does not support yet cross-language project managements. Of note, uv natively enforces the use of virtual environments when running Python scripts, see Table 2.3.
  2. The field renews fast -> stay alert, and up-to-date to the latest trends in this tech world.
Feature uv Poetry Pixi
Speed ⭐⭐⭐⭐ ⭐⭐ ⭐⭐⭐
Dependency management βœ“ βœ“ βœ“
Virtual environments βœ“ βœ“ βœ“
Python version install βœ“ βœ— βœ“
Package publishing ⚠ Acceptable ⭐ Best ⚠ Limited
Non-Python dependencies βœ— βœ— βœ“
CI performance ⭐⭐⭐⭐ ⭐⭐ ⭐⭐⭐
Maturity Medium High Medium
Table 2.3: Comparison of Python environment and dependency management tools
(a) Each tool used to have its perimeter, hence the diversity of Python execs
(b) The three levels of Python environments, from system-wide (not to be modified) to the project level
(c) Side-by-side compariosn of the core use cases of each Python tool -> uv supersedes them all.
Figure 2.4: Comparison of Python managers.

Main commands to replace old-fahsioned Python tools by uv.

Caricature illustrating the recent domination of uv

Decision tree for the choice of Python tool, depending on the scope: uv for pure Python projects (for instance, running bioinformatic analyses), poetry (and uv with less support) for Python packages, and pixi for cross-language projects. **Note that both conda and mamba ar eno longer required in the modern Programmer stack.
Figure 2.5

2.3.14.2 One Tool to bring them all and in the jungle of Python tool, bind them all: a uv story plot

I now describe the core steps to use the latest stable Python version (currently, 3.14), without breaking core Linux dependencies using pre-installed Python version.

  1. Install uv with the following command: curl -LsSf https://astral.sh/uv/install.sh | sh.
  2. Install latest Python version with uv: uv python install 3.14.
  3. Two configuration levels for setting up the Python version
  1. At the project level, run uv python pin 3.14.
  2. At the user level: bash cd ~ echo "3.14" > ~/.python-version
  1. Use uv instead of pipx to install core Python tools for package dependency, web IDEs, modern Python formatting and styling, …. As pipx, all these tools are automatically added to the user’s PATH:
uv tool install ruff ## ~ equivalent to pipx install ruff
uv tool install "dvc[ssh]" # recommended data management tool, and versining, if exceedging git-lfs
uv tool install black
uv tool install jupyterlab ## `JupyterLab` outdates previous `JupterNotebook` as a web-based, and user-friendly interface
uv tool install ipython
uv tool install pre-commit
uv tool install poetry
uv tool install cookiecutter `Cookiecutter` generates Python templates for modern packaging.
TipPython version management: core checks
  • Check integrity of system Python:
ls /usr/bin/python* ## -> ## only one version expected, Python 3.12 with modern Linux
/usr/bin/python3.12
  • Check version used by uv:
ls -la ~/.local/share/uv/python* ## path returned should be located within the HOME directory

Checking current Python version used:

  • From the terminal (system-wide), ls -d /usr/lib/python3.*, or which -a python should only return a unique version of Python, the one used by Ubuntu.

  • From a Python shell (including Jupyter Lab):

    import sys
print(sys.version)
print(sys.executable)
print(sys.path)

Relevant sources for Python tools

2.3.14.3 Marimo to replace Jupyter-Lab

  1. Install Marimo, including commonly used tools: duckdb (SQL cells), polars/pyarrow (SQL output), ruff (formatting), vegafusion (charts)
uv tool install "marimo[recommended]"

# Verify
marimo --version
  1. Add Cursor/VS Code extension:
cursor --install-extension marimo-team.vscode-marimo
  1. Commonly used keybindings to be added:
  // --- 🌊 Marimo ---
  // Open current .py file as a marimo notebook in the editor
  {
    "key": "ctrl+alt+m",
    "command": "marimo.openNotebook",
    "when": "resourceExtname == '.py'"
  },
  // Create a new sandboxed marimo notebook via terminal
  {
    "key": "ctrl+alt+shift+m",
    "command": "workbench.action.terminal.sendSequence",
    "args": { "text": "uvx marimo edit --sandbox \n" }
  },
  // Run current marimo notebook as a read-only app
  {
    "key": "ctrl+alt+r",
    "command": "workbench.action.terminal.sendSequence",
    "when": "resourceExtname == '.py'",
    "args": { "text": "uvx marimo run '${file}'\n" }
  }
  1. Interactive example is provided in demo.py.

2.3.15 Nextflow as workflow management tool

Installation process as standalone, and automatically up-to-date tool. ¡¡Check first that Java version at least 17 is installed, see Section 2.3.11:

curl -s https://get.nextflow.io | bash
chmod +x nextflow # make nextflow executable

# move nextflow into execubtale path
sudo mv nextflow $HOME/.local/bin/

2.3.16 Latex

sudo apt install texlive-full -y
## other commonly used packages
sudo apt install texlive-latex-extra texlive-fonts-recommended texlive-science biber latexmk -y

2.3.17 WhatsApp

  • No supported local Linux installation
  • Instead, recommended to use the Web version of WhatsApp, then pair it with your mobile device.

2.3.18 Cursor

  1. Download DEB extension.
  2. Run it:
sudo apt install ./cursor_2.0.77_amd64.deb
  1. Sync your Cursor configuration across devices, see Tip 2.3:
Tip 2.3: Export Cursor settings
  1. Export the core settings:
i.  Open Command Palette (`Ctrl/Cmd + Shift + P`), then search: **β€œPreferences: Open Settings (JSON)”**
ii. Export the file in your new device
iii. Default Linux installation: `~/.config/Cursor/User/settings.json`
  1. Export the keybinding shortcuts:
  1. Open: β€œPreferences: Open Keyboard Shortcuts (JSON)”
  2. Export keybindings.json into your local folder: ~/.config/Cursor/User/keybindings.json
  1. (the main difference with VSCode). Contrary to VSCode, you need to export the list of extensions manually:
  1. Retrieve the list of extensions running cursor --list-extensions > extensions.txt
  2. Install them back with:
grep -v '^\s*#' "~/.config/Cursor/User/extensions.txt" \
| grep -v '^\s*$' \
| xargs -I{} cursor --install-extension {}
  1. The whole list of extensions, and Cursor settings are available under the Cursor config folder.

More details are provide in Sync Cursor Settings the Dotfiles Way website, including the symlink commands tu fully automate this process

The harcore way, for syncing configuration files across numerous users, cf Benjamin, and Cursor Config Sync

2.3.19 Password Manager for Linux -> BitWarden

`BitWarden is the recommended password manager for Linux systems for a variety of reasons: it’s mostly free, compliant with most web browsers (Firefox, Chrome, Opera, …), including native Google password manager, and can sync your password database over an endless number of devices. There’s even a lightweight application for Iphone, and Android mobile phones. Besides, the storage expends beyond raw passwords, ranging from passkeys, to SSH secrets, or credit card information. Finally, it’s compatible with most OS, including Windows and Linux.

Accordingly, all these features fax expand the facilities delivered by native Ubuntu Gnome Passwords and Keys application manager, which besides can only be installed locally.

One major drawback, though, is that it does not check for duplicated values in an automated way.

Follow the following steps for its installation18

## Install Flatpak, and Gnome Flatpak plugin
sudo apt install flatpak
sudo apt install gnome-software-plugin-flatpak

## Add Flatbu repository for software storage
flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

## Install and run BitWarden locally
flatpak install flathub com.bitwarden.desktop
flatpak run com.bitwarden.desktop

## Install Web Add-on, going to https://chromewebstore.google.com/detail/bitwarden-password-manage/nngceckbapebfimnlniiiahkandclblb?hl=en, then pin in your Booktabs

## Export, then import your password database from other web browsers

In the Auto-fill tab of the Parameters configuration, leave unticked the option Do not auto-fill on page load + choose Default URI detection option as Exact to avoid ambiguities. Counterintuitively, go to Web Vault BitWarden to bulk remove passwords. This option is not proposed by default in the regular BitWarden.

2.4 Core numerical tools provided by AMU

List of numerical tools used in Amu

2.4.1 AMUZoom

  1. Retrieve latest version, choosing proper Linux distributions and OS architecture under Zoom downloads. Also avalaible online. Strongly recommended to install Zoom locally.
  2. Run sudo apt install ./zoom_amd64.deb
  3. Log-in using your university email address, using SSO. The account is provided with unlimited meetings available by default, use following domain: univ-amu-fr. 19

2 elements, listed below, to keep in in mind, when creating a Zoom meeting to enable any external user, with the password, to ling-in, and share its screen, see Figure 2.6:

Zoom first login

Zoom second step of login
Figure 2.6: Be careful about selecting the second, non-default option, if you want to allow external suers without any Amu mail address to connect on your Zoom session.

To go further, check the following online resources:

2.4.2 WooClap for QCMs

Go to Wooclap, and use your instutional mail adress for single sign-on across platforms.

2.5 Working with a remote server

id ${USER}
uid=1001(bastien) gid=1001(bastien) groups=1001(bastien),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),122(lpadmin),135(lxd),136(sambashare)
  • list of groups on the server, identify is defined by the combination of an username, UID (user ID), and GID (group ID) on both servers.
id ${USER}
uid=1007(bastienc) gid=1007(bastienc) groupes=1007(bastienc),1043(dtoo_project)

More information avalaible under Server Management tutorial.

2.5.1 Starting configuration

# ~/.bashrc (minimal and robust)

# Local user binaries first
export PATH="$HOME/.local/bin:$PATH"
export PATH="$PATH:$HOME/scripts/tools"

# Auto-switch interactive Bash sessions to user-local Zsh
if [ -x "$HOME/.local/bin/zsh" ] && [ -n "$PS1" ] && [ -z "$ZSH_VERSION" ]; then
  exec "$HOME/.local/bin/zsh" -l
fi

# -------------------------------------------------------------------
# Dotfiles migration via SCP (run these on your LOCAL machine)
# -------------------------------------------------------------------
# 1) Create target directories on server
# ssh mmg-server 'mkdir -p ~/.ssh'

# 2) Copy core dotfiles
# scp ~/.bashrc ~/.gitconfig mmg-server:~/

# 3) Copy SSH config
# scp ~/.ssh/config mmg-server:~/.ssh/config

# 4) Secure SSH permissions on server
# ssh mmg-server 'chmod 700 ~/.ssh && chmod 600 ~/.ssh/config'

# Optional: copy SSH keys (only if you explicitly want this)
# scp ~/.ssh/id_ed25519 ~/.ssh/id_ed25519.pub mmg-server:~/.ssh/
# ssh mmg-server 'chmod 600 ~/.ssh/id_ed25519 && chmod 644 ~/.ssh/id_ed25519.pub'
``

### SSH configuration

> Objective is dual: avoid typing your password each time you're connecting to a remote cluster, and keep a safe storage of all registered remote hosts:

1.  πŸ” Set up SSH remote access (with key-based auth)

``` bash
## remote server must have openssh-server installed
sudo apt install openssh-server
  1. Generate a pair of public-private SSH key on your local machine20
ssh-keygen -t ed25519 -C "your_email@example.com"

This creates:

- `~/.ssh/id_ed25519` (private key)
- `~/.ssh/id_ed25519.pub` (public key)

  1. Copy your key to the server with ssh-copy-id username@server_ip. You’ll no longer need typing your password once typed once.

  2. (Optional) Keep under ~/.ssh/config file the key features describing each remote cluster. For instance, my configuration for the IFB is the following, and to connect to it, I only need typing now ssh ifb-core. A second advantage of using this format for storing hosts is that it can be readily used by VS Code SSH Remote connection extensions.

## 🎯 alias for the host connection, either "ifb-core" or "ifb"
Host ifb-core ifb

  ## 🌍 The real hostname (or IP) of the remote server
  HostName core.cluster.france-bioinformatique.fr

  ## πŸ‘€ Username used on the remote machine
  User bchassagnol

  ## πŸ”‘ Path to your private SSH key
  IdentityFile ~/.ssh/id_ed25519

  ## 🚫 Force SSH to use ONLY the specified key above, avoiding complex managing of key version
  IdentitiesOnly yes

  ## πŸ”„ Order of authentication methods: SSH key, then keyboard-interactive, then fallback to password
  PreferredAuthentications publickey,keyboard-interactive,password

  ## πŸ€– Automatically add this key to ssh-agent when used
  AddKeysToAgent yes
  
# Host configuration for the new server
Host mmg-sb-05 new-mmg-cluster
HostName 139.124.156.52
Port 22218 # is the port, avoiding, unlike the popular 22, to be hacked.
User bastienc
IdentityFile ~/.ssh/id_ed25519
IdentitiesOnly yes
PubkeyAuthentication yes
PreferredAuthentications publickey,keyboard-interactive,password
AddKeysToAgent yes
ForwardX11 yes
ForwardX11Trusted yes

My host configuration, enabling by default graphical interfaces to run on the remote server, is avalaible under config-ssh

On older Ubuntu configurations, the shh-agent, and shh-add processes are not activated by default on startup. Check this by running systemctl --user enable ssh-agent.

Report to Table 2.4, and Figure 2.7 for further details

Practice Why
Prefer Ed25519 keys Small, fast, modern default.
Use a pass phrase on the key Protects the key if the disk is copied or stolen.
~/.ssh/config per host Aliases, and login recommendations
Never commit private keys Keep id_* out of git and cloud-synced folders.
ssh-copy-id once per host Standard way to populate authorized_keys.
Table 2.4: SSH recommended practices
Figure 2.7: Overview of an initial SSH connection
Option Purpose Effect on X11
-X X11 forwarding (untrusted) Runs GUI apps remotely
-Y X11 forwarding (trusted) Runs all GUI apps remotely
-C Compression Reduces network usage and can speed up GUI over slow connections
Table 2.5: Comparison side-by-side of the main options for customised sshconnexion

2.5.2 MMG cluster, and recommendations for project management

About projects timeline, and structure, follow these tips as soon as collaboration is involved:

  • Initiate git + github at the real start up of the project
  • Use only the /mnt/<cluster-name>/projects/ folder (no projects in your home, except for a quick run, and test)
  • When creating the project, set carefully group and user permissions, following guidlines of document https://github.com/BAUDOTlab/teaching_material/blob/main/Server%20Management/Server_Management.pdf, section Creating a New Project
  • Complement the README.md (to be created) at the root of the folder, with one short line per directory in the projects folder quickly summarising the overarching objective of the study

~/remote_project –>

Upon my recent transition from the Windows world to Linux, and huge frustration resulting from spending a lot of time recovering tutorials and disseminated configuration files when configuring a new laptop, here’s my detailed tutorial about best practices when starting from fresh on a Ubuntu session: https://baudotlab.github.io/teaching_material/Linux/installation-linux.html (and GH repo: https://github.com/BAUDOTlab/teaching_material) Beyond key commands, I distil some tips to enhance reproducibility across projects, provide default configuration tools for Git, RStudio and VS Code, and suggest software to replace the paying licence of the Office ecosystem. I also tried to concatenate recommendations from the team, including Benjamin, Morgane, Marielle, and philippe notably.

Besides, here are the 3 development guidelines that after discussions with Benjamin, might be the msot controversial, but strongly suggest nonetheless:

  • No further support of RServer, nor JupyterLab on the server -> with VS Code, and its extension β€œVisual Studio Code Remote - SSH”, it’s easy to automatically retrieve back its local programming framework

    • For Python, switch to VS Code (or Cursor for AI-guided development): Spyder is slow, and old-looking, Jupyter Notebooks is not reproducible (and limited in functionalities), especially witht he advent of Marimo: https://marimo.io/, PyCharm, while offering a slightly better developer experience, has a paying licence that limits its functionalities + all its features are covered by VS Code extensions
    • For R, RStudio is definitely the best (to quote Benjamin, β€œthat’s the utmost shame that the best IDE had been developed for the worst programming language”). But running it on the server implies strong latency -> suggested workflow: develop, and run your scripts on small examples locally, then scale them on larger datasets using VS Code on the server (or the command line)

  • Use uv for Python-full projects, uv or poetry for Python package development, and pixi for multi-language projects (see why in following caricature) -> especially, both conda and mamba are heavy, and way too slow

  • About projects timeline, and structure, follow these tips as soon as collaboration is invovled:

    • Initiate git + github at the real start up of the project
    • Use only the /mnt/<cluster-name>/projects/ folder (no projects in your home, except for a quick run, and test)
    • When creating the project, set carefully group and user permissions, following guidlines of document https://github.com/BAUDOTlab/teaching_material/blob/main/Server%20Management/Server_Management.pdf, section Creating a New Project
    • Complement the README.md (to be created) at the root of the folder, with one short line per directory in the projects folder quickly summarising the overarching objective of the study

Finally, if you: - Want to collaborate to the tutorial: favour quarto (or notebooks) editable files over PDFs, index your document under https://github.com/BAUDOTlab/teaching_material/blob/main/_quarto.yml. You can also report issues directly on the website, clicking on the option β€œEdit this page” in the footer - For computational nerds, or people generally interested in best programming guidelines, solving computational and dependency nightmares, or simply curious, add a like to this comment -> I’ll add a Slack channel to unify debates, and troubleshoot issue solving :-)

  1. Returns amd64 in my caseβ†©οΈŽ

  2. Alternatively, you can rely on the GNOME Interface, Wifi sectionβ†©οΈŽ

  3. Note that Comments must be placed in separated lines, not inline.β†©οΈŽ

  4. Accept as EOL CRLF, but always commit as LFβ†©οΈŽ

  5. constrain commits to be encoded and pushed as LFβ†©οΈŽ

  6. Detailled information is avalaible hereβ†©οΈŽ

  7. apt-get works similarly, but is now deprecatedβ†©οΈŽ

  8. Fetch the latest stable archive, extract it, and add executables to your PATH, see example under Section 2.3.12β†©οΈŽ

  9. Time-out units are reported in seconds, accordingly, this amounts to one hourβ†©οΈŽ

  10. default repo for third-party apps, preventing conflicts with distributed, native packagesβ†©οΈŽ

  11. You may configure the Java version used by default under Tools -> Options -> Advancedβ†©οΈŽ

  12. Alternatively, you also have the native Fonts manager tool under GNOME launch startβ†©οΈŽ

  13. On Ubuntu, a more modern version of Java, the 21, was installedβ†©οΈŽ

  14. Alternatively, download with curlβ†©οΈŽ

  15. What matters the most here is uniformity across platformsβ†©οΈŽ

  16. %AppData% is a shortened alias for this expanded path on Windows: C:\Users\<YourUser>\AppData\Roaming\RStudioβ†©οΈŽ

  17. If some of the setting changes were not applied, you can usually access them from the Menu options with Tools > Global Options...β†©οΈŽ

  18. Contrary to best guidelines suggested in Note 2.1, only the flatpak and snap installation are supported for Ubuntu devices -> no automatic updates with native apt Ubuntu dependency managerβ†©οΈŽ

  19. Alternatively, use the web version available hereβ†©οΈŽ

  20. Using a passphrase is not compuslory, but saferβ†©οΈŽ