This repo seeks to speed up setup time on new devices by consolidating configuration files for applications like tmux, rstudio, fish, etc all in the one place

1. Install the kitty terminal. Main benefit is it supports images!
2. (on mac) Install homebrew
3. brew install fish and set to default shell.
4. Set default shell

   echo /opt/homebrew/bin/fish | sudo tee -a /etc/shells
   chsh -s /opt/homebrew/bin/fish
   

5. Install fisher for fish plugin management
6. Install tide for a prettier prompt (don't forget to install the Nerd fonts as described on the bottom of the github readme)
7. If using alacritty mkdir -p ~/.config/alacritty; cp config/alacritty.toml ~/.config/alacritty
8. Install arf for a better R terminal.
9. If using arf, run arf config init to create config file and copy contents from arf/arf.toml

6. Install tmux for terminal multiplexing (brew install tmux)
7. Install tmux plugin manager
8. Install catpuccin-tmux theme 2.3.0

mkdir -p ~/.config/tmux/plugins/catppuccin
git clone -b v2.3.0 https://github.com/catppuccin/tmux.git ~/.config/tmux/plugins/catppuccin/tmux

9. Copy config/.tmux.conf to ~/.tmux.conf
10. Ctrl-b + r to reload tmux conf then Ctrl-b + I to install plugins

For kitty terminal, just copy config/kitty/ folder to ~/.config/kitty/. This will also set kitty to use a catppuccin macchiato theme.

1. Install neovim
2. Clone config by running git clone https://github.com/selkamand/nvim.git ~/.config/nvim
3. Compile tree-sitter-cli using cargo so it gets linked to your system glibc cargo install tree-sitter-cli (after you install rust)

I usually like having a folder of ~/scripts added to my path

# Add custom path to path
set -U fish_user_paths (realpath ~/scripts) $fish_user_paths

For scripts to add see: assorted_bash_utils

On linux, to replicate pbcopy/pbaste commands use the following aliases

alias pbcopy 'xclip -selection clipboard'
alias pbpaste 'xclip -selection clipboard -o'
funcsave pbcopy
funcsave pbpaste

Set R to open arf terminal

alias R arf
funcsave R

On most platforms, you'll need to make ls colourful

alias ls 'ls -G'
funcsave ls

and define ll (longlist) yourself

alias ll 'ls -lh'
funcsave ll

All of the following can be installed from brew

# Utilities
aria2 # fast downloads
htop # better top
parallel # parallelization utility

# Bioinformatics sofware
htslib  
samtools 
bcftools

## Containerisation / Virtualisation
docker
lazydocker # Terminal Interface for docker management

# Dependency Managers
micromamba # Complete conda rewrite in C++ for speed - no python dep :)
lmod # Dependency manager

Install this software all at once using

cat config/brew_software_list.txt | grep "^[a-zA-Z]" | cut -f1 -d ' ' | xargs -n 1 brew install

1. Install SDKman for fish
2. sdk install java

1. Install R and Rstudio
2. Copy config/.Rprofile to ~/.Rprofile so new packages have the right author info. If you're not the owner of this repo, either skip this or change .Rprofile to your information)
3. In Rstudio, edit snippets - than replace all with content from r.snippets

Can use Rswitch (on mac) to manage multiple R installs / renv for R package virtual environments.

If on a linux distro, always configure R to install binaries from the posit package manager (otherwise you tend to compile most from source!!). Some linux distros require you configure the R User Agent Header.

Install rust

My preferred way to manage python is pyenv (brew install pyenv)

• VScode for rust/python/js/bash dev.

1. Nextflow

See brew lmod page for initialisation instructions for fish.

Then set MODULEPATH variable as follows

mkdir -p ~/tools/modulefiles/
set -Ux MODULEPATH (realpath ~/tools/modulefiles/)     

• graphics card usage: nvtop
• hardware: inxi -Fxz