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https://github.com/martibosch/ubuntu-setup-guide
https://github.com/martibosch/ubuntu-setup-guide
Last synced: 19 days ago
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- Host: GitHub
- URL: https://github.com/martibosch/ubuntu-setup-guide
- Owner: martibosch
- Created: 2022-03-03T11:05:19.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2023-05-22T17:37:54.000Z (over 1 year ago)
- Last Synced: 2024-06-11T16:31:37.167Z (8 months ago)
- Size: 14.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Ubuntu setup guide
Tested for PopOs 22.04 LTS in a Lenovo Thinkpad X1 Carbon 8.
## 0. Basic configuration
### Battery thresholds
* Charge only up to 80% to improve battery lifespan: `sudo echo 80 | sudo tee /sys/class/power_supply/BAT0/charge_control_end_threshold`
## 1. Terminal
1. Install `zsh`, i.e., `sudo apt install zsh`.
2. Install [oh-my-zsh](https://github.com/ohmyzsh/ohmyzsh) and set it as default shell.
3. Log out and log back in.
## 2. Messaging and browsing
1. Install [Flatpak and add Flathub remote](https://flatpak.org/setup/Ubuntu) (a potential TLS error can be solved using `sudo apt install --reinstall ca-certificates`).
2. Install [Telegram using Flatpak](https://flathub.org/apps/details/org.telegram.desktop).
3. Install [Signal](https://signal.org/en/download/).
4. Install [Brave browser](https://brave.com/linux/#release-channel-installation) and use the sync code from Telegram/Signal saved messages.
5. Install [Slack using Flatpak](flatpak install flathub com.slack.Slack).
## 3. Git and GitHub
1. [Generate a new 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) and then [add it to your GitHub account](https://docs.github.com/en/authentication/connecting-to-github-with-ssh/adding-a-new-ssh-key-to-your-github-account).
2. Download gpg key from MEGA and import it, i.e., `gpg --import private.key`.
3. Trust the imported key by first checking its ID using `gpg --list-keys --keyid-format LONG`, then `gpg --edit-key `, enter `trust`, assign a decision (e.g., "5 = I trust ultimately"), enter `quit` and kill the gpg agent as in `gpgconf --kill gpg-agent` so that the changes take effect.
4. Configure git:
* set the [git user name and email](https://git-scm.com/book/en/v2/Getting-Started-First-Time-Git-Setup)
* add [signing key to git](https://docs.github.com/en/authentication/managing-commit-signature-verification/telling-git-about-your-signing-key), i.e., `gpg --list-keys --keyid-format=long` and `git config --global user.signingkey `
* set the name of the default branch to "main", i.e., `git config --global init.defaultBranch main`
* set git to sign all commits, i.e., `git config --global commit.gpgsign true`
* set git to `git config --global --add --bool push.autoSetupRemote true`
8. Download the [emacs gitignore file](https://github.com/github/gitignore/blob/main/Global/Emacs.gitignore) and set it as global gitignore, i.e., `git config --global core.excludesfile ~/Emacs.gitignore`
## 4. Docker
https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-22-04
## 5. Mamba
1. Install [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
2. Initialize the shell by running `mamba init` (ensure that the command modifies `.zshrc`, otherwise run `mamba init zsh`).
3. Set up the [`create_default_packages`](https://conda.io/projects/conda/en/latest/user-guide/configuration/use-condarc.html#config-add-default-pkgs) to include by default a set of packages in all conda environments by adding the following to the `.condarc` file:
```
create_default_packages:
- black
- jupytext
- pandoc
- pre-commit
- pyright
- ruff
- ipykernel
```
### Software to install in the base environment
1. Install the packages from the `environment.yaml` file, i.e., from the root of this repository, and within the base environment, run `mamba env update -f environment.yaml`.
2. Follow the instructions below for package-specific configuration.
#### Jupyter notebook
1. Generate the base configuration, i.e., `jupyter-notebook --generate-config`.
2. In the generated config file, uncomment the line with `c.NotebookApp.open_browser = True` and set it to `False`.
#### direnv
1. Update the `.zshrc` file to automatically activate it by adding:
```
# >>> direnv setup for zsh >>>
eval "$(direnv hook zsh)"
# <<< direnv setup for zsh <<<
```
#### AWS CLI
1. Configure the named profiles using the command `aws configure --profile `.
### Autocompletion for oh-my-zsh
#### Snakemake
Update the `.zshrc` file to activate autocompletion by adding:
```
# >>> snakemake autocompletion for zsh >>>
compdef _gnu_generic snakemake
# <<< snakemake autocompletion for zsh <<<
```
#### Terraform
Add the autocompletion setup to the zsh profile by running `terraform -install-autocomplete`
#### mamba
1. Clone the [esc/conda-zsh-completion repository](https://github.com/esc/conda-zsh-completion) at `$ZSH_CUSTOM/plugins/`, i.e.: `git clone https://github.com/esc/conda-zsh-completion ${ZSH_CUSTOM:=~/.oh-my-zsh/custom}/plugins/conda-zsh-completion`
2. Modify the `plugins` line of `.zshrc` and add `conda-zsh-completion`, e.g., `plugins=(git conda-zsh-completion)`
#### minikube
1. Add the autocompletion setup to the zsh profile. First ensure that the directory `~/.oh-my-zsh/completions` exists (otherwise create it), then run `minikube completion zsh > ~/.oh-my-zsh/completions/_minikube`.
#### kubectl
1. Add the autocompletion setup to the zsh profile. First ensure that the directory `~/.oh-my-zsh/completions` exists (otherwise create it), then run `kubectl completion zsh > ~/.oh-my-zsh/completions/_kubectl`.
#### Others
First, use the following command to print the completion folders ([credits to Andrej Friesen](https://www.ajfriesen.com/github-cli-auto-completion-with-oh-my-zsh/)):
```bash
print -l $fpath | grep completion
```
which should output something like:
```
/home//.oh-my-zsh/custom/plugins/
/home//.oh-my-zsh/completions
/usr/share/zsh/vendor-completions
```
Then, **after** the line with `source $ZSH/oh-my-zsh.sh` add the following lines to the `.zshrc` file:
```
# >>> completion (conda, github cli, minikube, kubectl...) >>>
autoload -U compinit
compinit -i
# <<< completion (conda, github cli, minikube, kubectl...) <<<
```
## 6. Emacs
1. Clone [the emacs setup](https://github.com/martibosch/.emacs.d), i.e., `git clone [email protected]:martibosch/.emacs.d.git` to the user's home directory.
2. Follow the installation steps in the `README.md` file.
3. To enable [directory and prompt tracking](https://github.com/akermu/emacs-libvterm#directory-tracking-and-prompt-tracking) for zsh, add the following lines to the `.zshrc` file:
```
# >>> vterm
if [[ "$INSIDE_EMACS" = 'vterm' ]]; then
alias clear='vterm_printf "51;Evterm-clear-scrollback";tput clear'
fi
vterm_printf() {
if [ -n "$TMUX" ] && ([ "${TERM%%-*}" = "tmux" ] || [ "${TERM%%-*}" = "screen" ]); then
# Tell tmux to pass the escape sequences through
printf "\ePtmux;\e\e]%s\007\e\\" "$1"
elif [ "${TERM%%-*}" = "screen" ]; then
# GNU screen (screen, screen-256color, screen-256color-bce)
printf "\eP\e]%s\007\e\\" "$1"
else
printf "\e]%s\e\\" "$1"
fi
}
vterm_prompt_end() {
vterm_printf "51;A$(whoami)@$(hostname):$(pwd)"
}
setopt PROMPT_SUBST
PROMPT=$PROMPT'%{$(vterm_prompt_end)%}'
# <<< vterm
```