生信入门 第二天

Homework of my day 2 study of BIC by 生信星球.

Content for today is Linux OS login and basic commands.

1. What is Linux

A open-sourced, free, stable, and safe operation system, accounting for 2.7% of the computer OS market.

1.1 Application Scenario

Mainly in supercomputers

1.2 Strict Authentication

1.3 Command line

Different from the graphic interface of Windows，the operation of Linux depends on the command lines.

1.4 Directory structure

2. Why to use Linux?

Because the upstream data processing is usually conducted by servers (high-performance computers) which are using Linux OS.

Omics data need Linux and R.

#. How to log in sever provided by DuoHua?

Log in by Mac:

ssh userid@ip

then put in PIN

3. A few very, very high frequency linux commands

3.1 pwd

pwd: print working directory

pwd  #显示当前路径

3.2 mkdir

mkdir: make directory

mkdir biosoft #backup bioinformatics software or packages
mkdir project #save working projects
mkdir tmp #save others
mkdir src # save source codes

3.3 ls

ls: list directory or file

3.4 cd

cd: change directory

cd project #go into project
cd - # go back to previous directory

cd tmp
cd #go back to home directory
cd tmp
cd ~ #go back to home directory
cd tmp
cd .. # go back to upper directory

3.5 vi

vi, create a new txt file (vi is the txt editor of linux)

cd tmp
vi hello_hello.txt

something wrong when I press esc.

I can not quit from vi mode.

I have to shut down the terminal and open a new one to log in again.

after searching for the command, the correct command should be press esc to quit edting mode, then press colon key to call out prompt, put in x, then enter to quit vi.

3.6 cat

cat hello_hello.txt
head -n 3 hello_wolrd.txt

3.7 cp

cp file1 file2 means copy file1 and rename it as file2.

cp hello_hello.txt hello2.txt
ls

cd ..
cp -r tmp tmp2 #copy whole directory
ls

3.8 mv

mv, move file to directory, or rename

cd tmp
ls
mv hello_hello.txt ../
cd ../
ls
mv hello_hello.txt hell3.txt
ls

3.9 rm

this is easy. I have used it in above practice when I made a wrong file or directory.

The End.