My configuration files on macOS

Install brew

Homebrew or Linuxbrew

Configurations managed by GNU stow

• bash install.sh
  • bash
  • git
  • perltidy
  • proxychains
  • GNU screen
  • vim
  • wget

macOS and Ubuntu

• brew.sh

  • Install CLI apps via Homebrew/Linuxbrew

• perl

  • bash perl/install.sh
  • bash perl/ensembl.sh

• python

  • bash python/install.sh

• r

  • bash r/install.sh

• rust

  • bash rust/install.sh

• Vim plugins

  • git clone https://github.com/VundleVim/Vundle.vim.git ~/.vim/bundle/Vundle.vim
  • vim +PluginInstall +qall

• Bioinformatics

  • download.sh
    • My repos, jkbin and circos
  • genomics.sh
    • Install apps from brewsci and my own homebrew-tap
  • others.sh
    • Install Trinity and interproscan manually

• TexLive

  • TinyTex
  • Fonts

macOS only

• macos.sh

  • Extracted from Mathias’s dotfiles

• brewcask.sh

  • Install GUI apps via Homebrew Cask

• Hammerspoon

  • Lua powered Mac window manager
  • bash hammerspoon/install.sh

• mpv

  • Video player I choose.
  • bash mpv/install.sh

Packages

The dir packages/ stores installed packages managed by various package managers.

• Homebrew

  • brew_tap.txt
  • brew_list.txt
  • brew_cask.txt

• Python pip_list.txt

• R r_list.txt

• node.js npm_list.txt

• VSCode vscode_list.txt

I'm writing them down here to make it easier to compare them between different machines and see if there are something missing.

mkdir -p $HOME/Scripts/dotfiles/packages
WHERE="$HOME/Scripts/dotfiles/packages"

# store
brew tap            | sort > ${WHERE}/brew_tap.txt
brew list --formula | sort > ${WHERE}/brew_list.txt
brew list --cask    | sort > ${WHERE}/brew_cask_list.txt

pip3 freeze > ${WHERE}/pip_list.txt

npm list -g --depth=0 > ${WHERE}/npm_list.txt

Rscript -e 'cat(.Library, "\n"); cat(.Library.site, "\n");' |
  xargs ls |
  sort -u \
  > ${WHERE}/r_list.txt

tlmgr list --only-installed --data 'name' > ${WHERE}/tlmgr_list.txt

code --list-extensions > $HOME/Scripts/dotfiles/packages/vscode_list.txt

# restore
pip install -r ${WHERE}/pip_list.txt

Plugins for cross-platform applications

• Firefox

  • fire-drag
  • Surfingkeys
  • Tampermonkey
  • uBlock Origin

• CLion

  • .ignore
  • CSV
  • EditorConfig
  • ini
  • Perl
  • Template Toolkit Support
  • Rust
  • Toml
  • PowerShell
  • R Language for IntelliJ
  • TeXiFy IDEA