Difference between revisions of "Linux"

Latest revision as of 19:41, 3 May 2017

Misc Links

These topics have their own pages.

Gnuplot

Common C, C++, FORTRAN Libraries

Octave Tutorial

Latex

Power User Tools

The Command Line

Useful Commands

The following is a (short) list of useful command when manipulating data in text files. Some common options are listed, but may not be explained. For full descriptions of each command, see the man page. stdin, stdout, and stderr refer to standard input, output and error, respectively.

File Management: Creating, Viewing, Moving, Deleting, Etc.

ls [dir]

list the contents of a directory to stdout

if no directory is given, the contents of the current directory are listed

common options: -l, -a

cd [dir]

change current working directory to a directory. i.e. go into a directory

used to navigate the filesystem

mkdir dir

make directory named 'dir'

rm file1 [file2 [...] ]

remove one or more files

if trying to remove a directory, the -r option must be given

mv source [source2 [...] ] dest

move a file or files. if multiple files are given, then the last argument must be a directory.

the move command will do different things depending on how many arguments are given, and whether the arguments are files or directories.

see a list of examples here

cp source [source2 [...] ] dest

copy a file or files. if multiple files are given, then the last argument must be a directory.

like the move command, cp will do different things depending on the arguments given. see the examples for mv to see how arguments determine the outcome.

cat [file1 [ file2 [...] ] ]

print text file(s) to stdout. if multiple files are given, their text is concatenated

useful for starting a pipeline of commands from the contents of a text file

find dir [options]

find files and directories

very powerful search utility for listing all files/directories below a given directory

useful options -name,-type

Processing Text Files

cat [file1 [ file2 [...] ] ]

print text file(s) to stdout. if multiple files are given, their text is concatenated

useful for starting a pipeline of commands from the contents of a text file

grep "pattern" [ file1 [ file2 [...] ] ]

find text matching 'pattern' in files, or from stdin, and print matching lines to stdout

useful for finding a file containing a specific configuration options

useful for filtering output of a program to only those lines that are interesting

see a list of examples here

echo [args...]

print arguments to stdout

useful for starting a pipeline of commands from a variable's value

useful for printing output to the terminal from inside a script

sort

read from stdin, sort lines, and write to stdout

common options: -k, -t, -n, -g

cut

read from stdin and write selected columns to stdout.

common options: -d, -f

column

read from stdin and write to stdout such that columns are aligned

common options: -t

head [file]

read from stdin, or from a file, and print the first 10 lines

useful for taking a peak at the contents of a large file

useful for limitng the output of a pipeline

common options: -n

tail [file]

read from stdin, or from a file, and print the last 10 lines

similar uses to head

can be used with head to print a single line, or range of lines, in a file

common options: -n

sed 's/old/new/g' [file]

read from stdin, or from a file, and replace all instances of 'old' with 'new', then print to stdout

gawk '{print $1,$2}' [file]

read from stdin, or from a file, and print columns (in this example, we would be printing columns 1 and 2).

gawk is often more useful than cut because it considers columns/fields to be separated by any white space

gawk can be used to re-order columns easily

gawk can be used to "transform" columns easily (for example, multiply a column by 2)

gawk gawk can be used to do much more than just print columns from a file. see a list of examples here

Pipes

Pipes allow you to use multiple commands together. Any command that reads input from stdin and writes to stdout can be used in a pipe. So, for example, if we wanted to sort a file and print it to the screen, we could do this two ways.

Either just use the sort command

user@host:~$ sort file.txt

or use cat and sort together with a pipe.

user@host:~$ cat file.txt | sort

We will most often use cat to start a pipeline of commands.

If we only wanted the first 10 lines of the sorted output, all we have to do is send it to head

user@host:~$ cat file.txt | sort | head

If we only wanted the first 5 lines, we just tell head to show only 5 lines.

user@host:~$ cat file.txt | sort | head -n 5

If we wanted to see the last 5 lines of sorted output, we could either reverse sort and use head, or use tail

 
 user@host:~$ cat file.txt | sort -r | head -n 5
 user@host:~$ cat file.txt | sort    | tail -n 5
 

Shell Scripts

Shell scripts are just text files that contain a list of commands for the shell to run. Anything you can run at the command line can be ran in a shell script. To create a shell script, you must do two things.

1. create a text file with the comment #! /bin/bash on the first line.
2. make the text file "executable" with the chmod command.

Here is an example of a simple "hello world" script.

#! /bin/bash

echo "hello world"

If you save this in a file named 'hello.sh', then to run it you must first make it executable.

user@host:~$ chmod +x hello.sh
user@host:~$ ./hello.sh

See the page on bash shell scripting here for information on writing scripts.