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Linux

Linux is a free and open source operating system released in 1991 under the GNU GPL license.

GPL allows anyone to use, modify and redistribute with the requirement that they pass it on with the same license.

Linux Shell

Shell is a command-line interpreter. There are several different shells (zsh, ksh, bust mostly bash)

Basic Linux Commands

  • . current directory
  • .. up directory
  • ~ home directory
command Usage
ls list files and directories
cd change directory
cp copy, cp -r for directory
mv move
mkdir make directory
rm remove, rm -r for directory

WARNING: There is no trash bin in command line！

Other Useful Commands

command Usage
man get manual of one command
--help use this parameter to get helpful information
e.g. ssh --help

Shortcuts on Command Line

Shortcut Usage
↑, ↓ previous and next command
Tab auto complete, twice for hint
Ctrl + c interrupt the application
Ctrl + z suspend the application
Ctrl + l clear
Ctrl + a move cursor to the start
Ctrl + e move cursor to the dnd
Ctrl + u erase before Cursor
Ctrl + k erase after Cursor

Wild Card *

e.g. ls *txt: get all txt file in this directory

Commands for Information

command Usage
whoami name of current user
pwd print working directory
hostname get name of the host

Commands for File Manipulation

  • less/more – read through the file without loading the entire file. Press spacebar to continue or q to quit.
  • touch – create an empty file
  • head – show the first few lines of the file
  • tail – show the last few lines of the file
  • cat – read through the file(s)
  • grep – search for patterns in a file or files
  • cut – separate file based on columns
  • comm/diff – compare and see the difference between the files. The files have to be sorted before using either of these commands.
  • split – splits file into smaller files based on the options
  • sort – sort the file base on the options selected.
  • wc - word count

Linux Permission

$ ls -l
lrwxrwxrwx. 1 xxx xxx   16 Jan  9 21:16 archive -> /archive/xxx/
drwxrwxr-x. 3 xxx xxx 4096 Jan 10 12:31 LinuxExercise
-rw-r--r--. 1 xxx xxx 1431 Jan 11 20:20 linux.md

type user permission group permission others permission

  • type
    • l link
    • d directory
    • - file
  • permission
    • r : open and copy
    • w : edit and delete
    • x : run the commands OR change into the directory if it is a directory
    • - : no this permission

Because the data is binary in computer. So are these permissions.

Special Permissions

  • g+s s in group:

Change Permission

  • chown – change the owner
  • chgrp – change the group
  • chmod – change read, write, and execute permissions
4210
rwx-

0 : --- none
1 : --x
2 : -w-
3 : -wx write and execute
4 : r--
5 : r-x read and execute
6 : rw- read and write
7 : rwx all the permission

e.g.

chmod 754 test.sh

# for me: 7, I can read it, edit it and execute it
# for my group, they can read it and execute it
# for others 4, they can only read

OR just

  • u user
  • g group
  • o others
  • a all

e.g.

chmod a+r test.sh # adds read permission for all classes
chmod o-x test.sh # removes execute permission for others
chmod u=rw,g=r,o= plan.txt # sets read and write permission for user, sets read for Group, and denies access for Others

jobs

  • suspend jobs: CTRL + z
  • run background
    • python hello.py &
    • if job is already suspended, just type bg
  • see all jobs and the job number jobs
  • run foreground
    • fg
    • fg %<job number>
  • see all jobs running on this computer top
  • stop kill %<job number>

Bash function

A Bash function is essentially a set of commands that can be called numerous times.

# cn for compute-node
# time memory CPU
cn () {
    case $# in # if the number of arguments equals to 
        0) srun --pty /bin/bash;;
        1) srun --time=$1:00:00 --pty /bin/bash;;
        2) srun --time=$1:00:00 --mem=$2GB --pty /bin/bash;;
        3) srun --time=$1:00:00 --mem=$2GB --cpus-per-task=$3 --pty /bin/bash;;
    esac
}
  • cn = srun --pty /bin/bash
  • cn 4 = srun --time=4:00:00 --pty /bin/bash
  • cn 2 4 = srun --time=2:00:00 --mem=4GB --pty /bin/bash
  • cn 1 16 4 = srun --time=1:00:00 --mem=16GB --cpus-per-task=4 --pty /bin/bash

You can also save scripts in ~/.local/bin/ and add it to PATH

# User specific environment
if ! [[ "$PATH" =~ "$HOME/.local/bin:" ]]
then
    PATH="$HOME/.local/bin:$PATH"
fi
export PATH

Tar and zip

tar

parameters:

  • -c : create
  • -x : extract
  • -f : filename
  • -u : archives and adds to an existing archive file
  • -v : verbose
  • -A : Concatenates the archive files
  • -z : zip, tells tar command that creates tar file using gzip
  • -r : update or add file or directory in already existed .tar file
  • -t : displays or lists files in archived file

e.g.

$ tar cf md.tar *.md # create tar file

$ tar ft md.tar # list all files in the tar
README.md
bio-on-arm-linux.md
bio-on-vps.md
hpc.md
linux.md
singularity.md
ssh.md
vim.md

$ tar czf md.tar.gz *.md # create a tar file with gzip

$ ls -lh *.tar # gzip is smaller
-rw-r--r-- 1 zzz zzz 14K Feb 13 19:02 md.tar.gz
-rw-r--r-- 1 zzz zzz 40K Feb 13 18:57 md.tar

$ tar xfv md.tar.gz # extract
README.md
bio-on-arm-linux.md
bio-on-vps.md
hpc.md
linux.md
singularity.md
ssh.md
vim.md

gzip, gunzip, and zip

  • g zip
  • g unzip
$ gzip cele.fastq # gzip file

$ gunzip cele.fastq.gz # g unzip

$ gunzip -c cele.fastq.gz > cele.fastq # keep original gzip file
  • zip
  • unzip
$ zip temp.zip file1 folder2

$ unzip temp.zip