A Practical cheat sheet

Command Description Usage example
echo Print out a string to screen Echo 'Hello World'
man Look at the manual page of a command man man
clear Clear the screen clear
<tab> Complete a path or command <tab>
cd Change directory cd /directory/path/
pwd Print Working Directory pwd
ls List the contents of a directory ls /directory/path/
mkdir Make a directory mkdir /directory/path/new_directory/
cp Copy content to another path cp /directory/path/file.txt /directory/path/new_directory/
mv Move content to a new path mv /directory/path/file.txt /directory/path/new_directory/
rm Delete content rm /directory/path/file.txt
cat Print contents of a file to screen cat /directory/path/file.txt
head Print out the first n lines of a file to screen head -n 10 /directory/path/file.txt
tail Print the last n lines of a file to screen tail -n 12 /directory/path/file.txt
less Read a file one page at a time less /directory/path/file.txt
wc Print out line, word and byte count wc /directory/path/file.txt
grep Search for lines that contain a specific pattern grep "pattern" /directory/path/file.txt
vim Text editor vim /directory/path/file.txt

B Windows terminals

If you are on a windows you may need to download a terminal program to ssh to a linux cluster. Thankfully Macs come with an in built terminal. Below are a few suggestions of windows terminals:

C ssh

The ssh (Secure Shell Protocol) command is used to login into cluster and other machines. For more information on this please see the following online tutorial: https://opensource.com/article/20/9/ssh

D File transferring

When working with a remote cluster you will most likely want to transfer files from your computer to the cluster and vice versa.

For transferring on windows machine I would suggest WinSCP.

For transferring on Macs I would suggest FileZIlla

E Mamba

E.1 Mamba installation

Once you start using bioinformatic tools you will notice that a lot of installing is required. I would highly suggest using Mamba for this purpose.

Mamba is a reimplementation of conda. It is a great tool for installing bioinformatic packages including R packages.

Mamba github: https://github.com/mamba-org/mamba

The best way to use Mamba is to install Miniforge. It has both Conda and Mamba commands.

Miniforge installation: https://github.com/conda-forge/miniforge

Mamba guide: https://mamba.readthedocs.io/en/latest/user_guide/mamba.html

F vim

To enter the vim text editor you can use the command vim. The command is: vim file.txt.

vim can be run with a previous file name which you can then edit or a new file name in which case you will create a new file.

Once you are in the vim editor there are two main modes:

  1. Command mode: This is the starting mode of vim. It can be used to enter commands but not for typing.
  2. Insert mode: This mode can be used to insert characters into the text. Pasting only works properly in insert mode. You will know you are in insert mode as at the bottom of the screen will be “-- INSERT --”.
    1. To enter insert mode press i
    2. To escape Insert mode press esc

Below are a subset of commands you can use in the command mode of vim.

  • :q - Quit vim. Will fail if there are any unsaved changes
  • :w - Save the file
  • :wq - Save and quit
  • :x - Save and quit
  • :q! - Quit and throw away unsaved changes
  • :saveas file - Save file as. File name can be changed
  • :w file - Save file as. File name can be changed
  • arrow keys - Navigate the text. (works in insert mode too)
  • ^ - Jump to the start of a line
  • $ - Jump to the end of a line
  • /pattern - Search for pattern
  • n - Repeat search in same direction
  • N - Repeat search in reverse direction
  • dd - Delete the current line
  • i - Enter insert mode
  • 1G - Go to the first line in the file. Number can be changed
  • G - Go to the last line of the file

Vim cheatsheet