basic shell commands

the Unix shell

Go to software carpentry introduction and do

setup to download the data and open a terminal

After you do the setup and have a terminal open, type echo $SHELL. You may see this:

$ echo $SHELL
/bin/bash

or you may get this:

% echo $SHELL
/bin/zsh

The terminal is the “window” (more or less), while the shell is a program (or a programming language, like R and Python are). There are several shell programs, bash (and zsh) being the most common. They are almost equivalent.

bash for “Bourne-Again SHell”, pun on the name of the developer of the original Unix shell, Stephen Bourne.

Then do:

navigating files and directories
working with files and directories
- do things on your own laptop. watching or reading ≢ practice.
- ask others on Piazza, or in office hours.

summary

directory structure, root is /
relative versus absolute paths
- in your code and projects: use relative paths as much as possible: it makes your code more portable, for others, and for yourself if you re-locate your own project folder
shortcuts: ., .., ~, -
- cd - is so useful!
tab completion to get program and file names
up/down arrows and ! to repeat commands


`whoami`	who am I? to get your username
`pwd`	print working directory. where am I?
`ls`	list. many options, e.g. `-a` (all) `-l` (long) `-lrt` (reverse-sorted by time)
`cd`	change directory
`mkdir`	make directory
`rm`	remove (forever). `-f` to force, `-i` to ask interactively, `-r` recursively
`rmdir`	remove (delete) directory, if empty
`mv`	move (and rename). can overwrite existing files, unless `-i` to ask
`cp`	copy. would also overwrite existing files
`touch`	create blank file, or modify time stamp of existing file
`diff`	difference
`wc`	word count: lines, words, characters. `-l`, `-w`, `-c`
`cat`	concatenate
`less`	because “less is more”. `q` to quit.
`sort`	`-n` for numerical sorting
`head`	first 10 lines. `-n 3` for first 3 lines (etc.)
`tail`	last 10 lines. `-n 3` for last 3 lines, `-n +30` for line 30 and up
`uniq`	filters out repeated lines (consecutive). `-c` to get counts
`cut`	cut and return column(s). `-d,` to set the comma as field delimiter (tab otherwise), `-f2` to get 2nd field (column)
`echo`	print
`history`	shows the history of all previous commands, numbered
`!`	`!76` to re-execute command number 76 in the history, `!$` for last word or last command

file names

so important: no spaces! example:

create a directory ‘raw sequences’ in data, using a GUI (e.g. Finder)
try to remove it from the command line:

cd data
ls
rm -rf raw sequences

lucky for us: raw or sequences didn’t exist (chainsaw…)
how can we remove this directory?

prefer lower-case letters, especially for the first letter of a file name: time saver, along with tab completion
common usage: capitalize between words, or underscores, or -, like wheatSequenceAlignments (camel case style) or wheat_sequence_alignments (snake case style).
use ASCII characters only, no space (did I mention this already?), no /, no \ (for Windows), no - for the first character.
R users: avoid dots. conventionally used for the file extension.

Great presentation by Jenny Bryan

choose file names to ease automation, using shell expansion
use leading zeros: file-0021.txt rather than file-21.txt. lexicographic sorting files (like with ls) would otherwise place file-1390.txt before file-21.txt.
file extensions:
- not needed by the computer. for humans only.
- explicit is better than implicit for humans. ex: rice_genes.fasta versus rice_genes
- used by the computer occasionally: to pick the ‘default’ app to open a file (e.g. open xxx.pdf or xdg-open xxx.pdf); to color parts of text by a text editor; etc.

typing skills

had keyboarding classes in elementary school?
it’s like talking or walking: it’s assumed.
take a test
invest in your typing skills! it will save you time and stress.
allow yourself two weeks to be slow.

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