# A. Set up new computer with Ubuntu ## 1. From the web #### 1.1 **Sign into Github** + Sign in, make an [ssh key](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent) + [Add to github](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account) #### 1.2 **Starship prompt** + Install [NerdFont](https://www.nerdfonts.com/font-downloads) like FiraCode, move to `./fonts` + Go [starship.rs](starship.rs) and follow the instructions #### 1.3 **Conda**. Install miniconda and poetry ```shell= mkdir -p ~/installs # if not available cd ~/installs wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh bash Miniconda3-latest-Linux-x86_64.sh # follow instructions # sometimes the following will be necessary conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r ``` #### 1.4 **Dropbox** from [here](https://www.dropbox.com/en_GB/install-linux). If possible, install in the `/data` folder #### 1.5 **Brave browser**: Download from website, set as main browser. #### 1.6 **Kitty terminal** + Install from [here](https://sw.kovidgoyal.net/kitty/binary/) + Add relevant things to path: `sudo ln -s ~/.local/kitty.app/bin/kitty /usr/local/bin/kitty` (also `kitten`) #### Optional from web **1password**: Download `deb` file from the website and then run `sudo apt install ./1password-latest.deb` ## 2. From `apt` Run the following command: ```shell= sudo apt install build-essential imagemagick pcmanfm rofi conky tldr neovim texlive libreoffice -y ``` Finish with `tldr -u` to update the database for `tldr`. you have just installed the following: | Name | id for `apt` | Description | | -------- | -------- | -------- | | Build Essentials | `build-essential`| C, C++, etc | | ImageMagick | `imagemagick` | Utils for image analysis | | pcmanfm | `pcmanfm` | File manager | | rofi | `rofi` | Run prompt | | conky | `conky` | Graphics and stuff | | tldr | `tldr` | Easier `man` pages | | NeoVim | `neovim` | Text editor | | TeX Live | `texlive` | LaTeX libraries | | LibreOffice | `libreoffice` | Office | #### 2.1 Sometimes this might be needed ```shell= sudo apt install qtwayland5 -y ``` ## 3. Rust/cargo utils These are really fast utilities to make your life easier. They substitute some of the linux core-utils like `ls`, `grep`, etc. #### 3.1 Install Go [here](https://doc.rust-lang.org/cargo/getting-started/installation.html). Once installed, add to the path with: ```shell . "$HOME/.cargo/env" ``` #### 3.2 Actual programs to install: Install the following: ```shell cargo install exa fd-find ripgrep bat ``` | Name | id for `apt` | Description | | -------- | -------- | -------- | | EXA | `exa`| Substitute for `ls` | | fd | `fd-find` | Easier to use substitute for `find` | | ripgrep | `ripgrep` | Easier to use substitute for `grep` | | bat | `bat` | Nicer looking substitute for `cat` | Now, make `exa` super useful by adding the following to the `.bashrc` file ``` alias exa='exa -la --group-directories-first' ``` ## 4. From snap **VSCode** `sudo snap install code --classic` **Slack** `sudo snap install slack` ## 5. From Github ### **Configration files** `myconfig` ```shell mkdir -p ~/utils git clone git@github.com:alonsoJASL/myconfig.git ~/utils/myconfig cd ~/utils/myconfig ``` + Copy config folder`cp -R rofi ~/.config/` + Move Starship TOML `cp starship.toml` + KITTY: move contents from `kitty` to `~/.config/kitty/` + CONKY: move contents from `conky` to `~/.config/conky`, then setup conky as startup application `$HOME/.config/conky/start_conky.sh` + BASHRC: get whatever is needed from `.bashrc` file. + COLORSCRIPT: apply the patch (see below) ### 6. (OPTIONALS) Colorscript and Wallpapers If you haven't, do `mkdir -p ~/.installs`, and inside do: ```shell git clone https://gitlab.com/dwt1/shell-color-scripts.git git clone https://gitlab.com/dwt1/wallpapers.git ``` For `colorscript`, do a `sudo ln -s PATH/colorscript.sh /usr/local/bin/colorscript`. Add the line to the `.bashrc` ```shell colorscript -r ``` # B. Important development configs These come after you've installed everything else. By this, make sure you have a `~/dev` and an `~/installs` folders. Inside `dev` ``` ➜ ls ~/dev/ build myconfig python src ``` ## cemrg-heartbuilder ```shell= cd python/ git clone git@github.com:OpenHeartDevelopers/cemrg-heartbuilder.git cd cemrg-heartbuilder/ conda create -n cemrg-heartbuilder python=3.10 -y conda activate cemrg-heartbuilder poetry config virtualenvs.create false --local poetry install ./setup.sh ``` ## imatools ```shell= git clone git@github.com:alonsoJASL/imatools.git cd imatools/ conda env create -f environment.yaml conda activate imatools poetry install ./setup.sh ``` ## meshtool ```shell= git clone https://bitbucket.org/aneic/meshtool.git cd meshtool/ make # then link it to /usr/local/bin sudo ln -s $(pwd)/meshtool /usr/local/bin/meshtool ``` ## itk-snap (and c3d) Download and move the compressed file to the `~/installs` folder ```shell= mv ~/Downloads/itksnap-4.2.2-20241202-Linux-x86_64.tar.gz ~/installs/ cd ~/installs tar xvf itksnap-4.2.2-20241202-Linux-x86_64.tar.gz # Extract ``` Create an `alias` on your `.bashrc` pointing to the binaries for `itksnap` and `c3d`. A symlink does not work in this context. ## Paraview ```shell= mv ~/Downloads/ParaView-5.13.3-MPI-Linux-Python3.10-x86_64.tar.gz ~/installs/ cd ~/installs tar ParaView-5.13.3-MPI-Linux-Python3.10-x86_64.tar.gz cd ParaView-5.13.3-MPI-Linux-Python3.10-x86_64/bin sudo ln -s $(pwd)/paraview /usr/local/bin/paraview ``` ## Meshalyzer ```shell= sudo apt install libfuse-dev mv ~/Downloads/Meshalyzer-5.4-x86_64.AppImage ~/installs/ cd ~/installs mkdir Meshalyzer mv Meshalyzer-5.4-x86_64.AppImage Meshalyzer/ cd Meshalyzer chmod +x Meshalyzer-5.4-x86_64.AppImage sudo ln -s $(pwd)/Meshalyzer-5.4-x86_64.AppImage /usr/local/bin/meshalyzer ``` ## CemrgApp Follow the instructions in the [wiki](https://github.com/OpenHeartDevelopers/CemrgApp/wiki/Build-CemrgApp-from-Scratch) ## Docker Follow the instructions in the [docs](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository) # Shortcuts + <kbd>SUPER</kbd>+<kbd>R</kbd> : `rofi show -run -normal-window` + <kbd>SUPER</kbd>+<kbd>W</kbd> : `rofi show -window -normal-window` + <kbd>SUPER</kbd>+<kbd>Return</kbd> : `kitty` + <kbd>SUPER</kbd>+<kbd>Q</kbd> : Exchange for the one that closes apps + <kbd>SUPER</kbd>+<kbd>F</kbd> : Opemn `pcmanfm` # Optional Remove the dock on Ubuntu: `sudo apt remove gnome-shell-extension-ubuntu-dock` Fix Nvidia driver from nouveau (ew) to nvidia: ```shell= ubuntu-drivers devices # Install the recommended driver sudo ubuntu-drivers autoinstall # OR if you want to be more specific (check output from step 2): # sudo apt install nvidia-driver-535 sudo reboot ``` Once you rebooted, check ```shell= nvidia-smi lsmod | grep nouveau # should be empty ``` # C. Imperial-specific ## Login to computer through ssh ### Setup (only do once) You need to install [OPKSSH](https://github.com/openpubkey/opkssh) ```bash= # LINUX curl -L https://github.com/openpubkey/opkssh/releases/latest/download/opkssh-linux-amd64 -o opkssh chmod +x opkssh # macOS curl -L https://github.com/openpubkey/opkssh/releases/latest/download/opkssh-osx-amd64 -o opkssh chmod +x opkssh ``` Initialise: ```bash= ./opkssh login --create-config ``` You'll need to install the imperial config file and save it to the `config.yml` that got created in the previous step: ```bash= curl https://rhn.cc.ic.ac.uk/install/scripts/standalone/sshgw/opkssh/config.yml -o ~/.opk/config.yml ``` ### Every time you want to log in > Certificate lasts 24 hours, so you need to do this pretty much every time ```bash= opkssh login ``` Follow instructions, you'll authenticate on the browser. This will create a pair of files in your `~/.ssh` folder (called `id_ecdsa`). Now, you can log in: ```bash= ssh <username>@opkssh.ic.ac.uk -i ~/.ssh/id_ecdsa ```