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bash

is bourne again shell

shortcuts

Command-Line Keystrokes

| ------ | ------| |Keystroke |Action| |CTRL-B| Move the cursor left| |CTRL-F |Move the cursor right| |CTRL-P| View the previous command (or move the cursor up)| |CTRL-N |View the next command (or move the cursor down)| |CTRL-A| Move the cursor to the beginning of the line| |CTRL-E| Move the cursor to the end of the line| |CTRL-W |Erase the preceding word| |CTRL-U |Erase from cursor to beginning of line| |CTRL-K| Erase from cursor to end of line| |CTRL-Y |Paste erased text (for example, from CTRL-U)|

cat

  1. input and outoput streams - standard input and output stdin stdout streams flexible
    1. input file device terminal window output stream of a process
    2. output
    3. standard error

cp

cp file1 file2 cp file dir cp file1 file2 file3 dir

touch

For example, to create an empty file, enter this:

touch file

rm

rm -r dir to delete a directory and its contents

cd

The cd command is a shell built-in. It wouldn’t work as a separate program because if it were to run as a subprocess, it could not (normally) change its parent’s current working directory. This may not seem a particularly important distinction at the moment, but there are times when knowing this fact can clear up confusion.

mkdir

rmdir

globbing

    at* expands to all filenames that start with at. *at expands to all filenames that end with at. at expands to all filenames that contain at.
  2. ? b?at matches boat and brat

grep

  1. to print the lines in the /etc/passwd file that contain the text root, enter this: grep root /etc/passwd
  2. For example, if you want to check every file in /etc that contains the word root, you could use this command: grep root /etc/*
  3. options
    1. -i for case senstive matches
    2. -v for inverting the search
    3. -w for looking for the exact word
  4. if you want to search more than 1 word and
    1. search 'grep -w "123456|123457"'
  5. regular expressions .* matches any number of characters, including none (like the * in globs and wildcards). .+ matches any one or more characters. . matches exactly one arbitrary character.
  6. to look in tar file use zcat zcat clinvar.vcf.gz | grep -w "1559177278"

pwd

-P for full path

diff

file

to check the format of the fiel

find

find dir -name file -print

less

To page through a big file like /usr/share/dict/words, you can use the command less /usr/share/dict/words. When running less, you’ll see the contents of the file one screenful at a time. Press the spacebar to go forward in the file and press b (lowercase) to skip back one screenful. To quit, press q.

ln

ln -s target linkname The linkname argument is the name of the symbolic link, the target argument is the path of the file or directory that the link points to, and the -s flag specifies a symbolic link

ls

-a = for dot files

ctrl d vs ctrl c Pressing CTRL-D on an empty line stops the current standard input entry from the terminal with an EOF (end-of-file) message (and often terminates a program). Don’t confuse this with CTRL-C, which usually terminates a program regardless of its input or output

getting help with man

man ls man -k keyword info command | less

environment variable

An environment variable is like a shell variable, but it’s not specific to the shell. All processes on Unix systems have environment variable storage. The main difference between environment and shell variables is that the operating system passes all of your shell’s environment variables to programs that the shell runs, whereas shell variables cannot be accessed in the commands that you run.

PATH

PATH is a special environment variable that contains the command path (or path for short), a list of system directories that the shell searches when trying to locate a command. For example, when you run ls, the shell searches the directories listed in PATH for the ls program. If programs with the same name appear in several directories in the path, the shell runs the first matching program.

If you run echo $PATH, you’ll see that the path components are separated by colons (:) PATH=dir:$PATH --> to add first look directories PATH=$PATH:dir --> to append the list Windows in git bash, while using windows, you need to add export PATH in the bashprofile

  1. To append path permanently in the linux
    1. nano ~/.bashrc this file will open up and at the end of it add the below line export PATH="path of the directory:$PATH"
    2. now save changes by exiting
    3. source ~/.bashrc
    4. echo $PATH now you can see your path being added up

SHell Input and Output

  1. command command > file command >> file To send the standard output of a command to the standard input of another command, use the pipe character (|)

  2. standard error You can redirect the standard error if you like. For example, to send standard output to f and standard error to e, use the 2> syntax, like this: ls /fffffffff > f 2> e

  3. standard input redirection To channel a file to a program’s standard input, use the < operator: head < /proc/cpuinfo

  4. Background processes: Normally, when you run a Unix command from the shell, you don’t get the shell prompt back until the program finishes executing. However, you can detach a process from the shell and put it in the “background” with the ampersand (&); this gives you the prompt back

    1. gunzip file.gz &

permissions

or example, to add group (g) and world (o, for “other”) read (r) permissions to file, you could run these two commands: chmod g+r file chmod o+r file Table 2-4: Absolute Permission Modes

Mode Meaning Used for 644 user: read/write; group, other: read files 600 user: read/write; group, other: none files 755 user: read/write/execute; group, other: read/execute directories, programs 700 user: read/write/execute; group, other: none directories, programs 711 user: read/write/execute; group, other: execute directories

compressing and archiving

formats

| ----- | -----| | format | | | gz | | | tar | | | xz | | | bz2 | |

  1. gzip

    1. single file only
    2. gzip
    3. gunzip

  2. tar: works like zip tar cvf archive.tar file1 file2 file3 cvf c = crate mode v = verbose diagnostice output print name of files and directories another v = file size permissions f = file option xvf x = extract t to check the content table p to preserve permission

  3. gunzip -dc file.tar.gz | tar xvf -

  4. zcat file.tar.gz | tar xvf -

  5. tar ztvf file.tar.gz

Reference books

  1. Learning the UNIX Operating System
  2. UNIX for the Impatient
  3. The Linux Command Line
  4. If you like math and are interested in where regular expressions come from, look up Introduction to Automata Theory, Languages, and Computation, 3rd edition, by Jeffrey Ullman and John Hopcroft (Prentice Hall, 2006).
  5. Learning the vi and Vim Editors: Unix Text Processing, 7th edition, by Arnold Robbins, Elbert Hannah, and Linda Lamb (O’Reilly, 2008), can tell you everything you need to know about vi. For Emacs, use the online tutorial: start Emacs, press CTRL-H, and then type T. Or read GNU Emacs Manual, 18th edition, by Richard M. Stallman (Free Software Foundation, 2018).