.. _making-your-linux-life-easier: Making your Linux life easier ============================= Here are some tips that you might not have picked up from introductory command-line tutorials. Aliases ------- You can put any bash commands you’d like into an alias (see http://tldp.org/LDP/abs/html/aliases.html for more). For example, to log in to biowulf by typing ``b``, use: .. code-block:: bash alias b="ssh -X $USER@biowulf.nih.gov" To change to a frequently-visited directory, .. code-block:: bash alias N="cd /data/project/" Middle-click paste ------------------ This is frequently overlooked in intro Linux tutorials, but in most software on Linux when you highlight text it goes into a separate copy buffer that can be pasted with middle-mouse-button. This means you effectively have two buffers, the typical Ctrl-C/Ctrl-X/Ctrl-V as well as the last-selected text buffer. This will work if you're on a Linux graphical user interface, for example if you're using `NoMachine to log in to Biowulf `_. Ctrl-C in terminals ------------------- To interrupt a command, use Ctrl-C. To paste text from the Ctrl-C/X/V buffer, use Ctrl-Shift-C or Ctrl-Shift-V (using most terminal emulators). If you're using tmux, it gets a little trickier -- see the :ref:`tmux` section for more. Opening files on Mac -------------------- Use ``open`` on Mac to open the file in the appropriate program, e.g., ``open document.docx`` to open in Word. Opening HTML files ------------------ When a URL shows up somewhere in the terminal, depending on your terminal you can easily open it on your local machine: - macOS Terminal app: Commad-double-click - iTerm2 app: Command-click - Alacritty: click dotfiles -------- "Dotfiles" collectively refers to the various configuration files used by bash (``.bashrc``, ``.bash_profile``), git (``.gitconfig``), tmux ``.tmux.conf``), vim (``~/.vimrc`` or ``.config/nvim/init.vim``), and others. To prevent them from showing up in a standard ``ls`` call, they start with a leading ``.``, hence dotfiles. You can grow your own over time, or see https://github.com/daler/dotfiles to start with “the works”. Ctrl-R ------ Ctrl-R lets you search through your history. It works in the R interpreter, too. See ``fzf`` below in the tools section for a fancier way for searching through history. Tools ----- Here are some useful tools to install. If you're using `my dotfiles `_, you can use the ``setup.sh`` script to easily install them. visidata ~~~~~~~~ We work a lot with TSV files and we work a lot on the command line. Things like ``less`` and ``vim`` don’t format the data as nice as a spreadsheet program like LibreOffice Calc or Gnumeric do. `visidata `_ formats TSV files into a browsable, sortable table with all sorts of convenient hotkeys. Makes it trivial to find the most strongly differentially expressed genes from a TSV of DESeq2 results. See a lightning demo `here `_. .. _tmux: tmux ~~~~ Start tmux when you're on a remote host (like `Biowulf `_), and you'll get a persistent terminal. That means you can lose the connection, or shut your laptop off and when you reconnect to the remote host, when you reattach to the tmux session you'll have everything exactly where it was -- running programs will keep running on the host even when you're not logged in with your laptop. In addition, you can split the full-screen terminal window into panes or collections of panes, effectively getting multiple terminals that you can quickly switch between. This makes it great to, for example, have a file open in a text editor in one pane while testing it out at the command line in another pane. - Brief guide to tmux: https://medium.com/actualize-network/a-minimalist-guide-to-tmux-13675fb160fa - Lots more details: https://leanpub.com/the-tao-of-tmux/read - Recent HN post: https://news.ycombinator.com/item?id=17998649 Copy/paste between tmux, vim/neovim, and the system clipboard can get a bit crazy. See http://www.rushiagr.com/blog/2016/06/16/everything-you-need-to-know-about-tmux-copy-pasting-ubuntu for the details. fzf ~~~ `fzf `_ is a fuzzy-finder. The installation script will make Ctrl-R, for searching through history, use ``fzf``. Any content can be piped through fzf -- see the home page for all sorts of ways it can be used. ripgrep ~~~~~~~ `ripgrep `_ is like grep combined but much faster. Perfect for looking through source code since it plays nice with git repos -- for example, it will ignore searching in files added to ``.gitignore`` or will avoid searching in huge files.