Introduction To Linux

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1 Introduction To Linux Using The Command Line David To Biomedical Research Centre for Mental Health 2nd December

2 What Is Linux? UNIX-like operating system using the Linux Kernel: and GNU project tools Linux Kernel: originally written by Linus Torvalds in 1991 GNU Project: originally announced by Richard Stallman in 1983 Open source and free. Released under the GNU General Public License Linux Mascot: Tux Today it is used in many environments Industry, entertainment, research GNU Mascot: Heckbert Servers, desktops, mobile devices, video game consoles, super computers 2

3 The History Of UNIX 3

4 Popular Linux Distributions There are many distributions of linux For beginners, Ubuntu or Fedora are probably the easiest to use 4

5 The Command Line Provides a way to control the computer via the keyboard May seem archaic (it is!) but is very powerful, and can be much quicker than a graphical user interface (GUI) Don't be scared! 5

6 Using OpenSSH OpenSSH allows you to establish a secure connection to a remote computer Windows users can use the Putty Application Windows Linux & Mac OS X users can use the Terminal application To connect you'll need a minimum of 2 things Linux IP Address/Hostname of the remote computer Login & Password Mac OS X 6

7 Using OpenSSH laptop.home.co.uk Internet ssh connection tcp port 22 remotehost.kcl.ac.uk Command: ssh OpenSSH SSH client (remote login program) ssh (connect with username dto to remote host remotehost.kcl.ac.uk) ssh -l dto remotehost.kcl.ac.uk (same as above, but different style) ssh -p (same as above but use port 51515) 7

8 Using Putty 8

9 Logging Out When you have finished with your connection, you should log out Command: exit 9

10 The Shell & Changing Your Password The command prompt is called a shell Shells: sh, ksh, csh, zsh, bash - We ll use bash Not just an interface to the computer, also a scripting language allows automation of tasks You enter your commands at the command prompt: $ Changing your password: Stand alone machine: passwd Server: yppasswd (NIS), kpasswd (kerberos) 10

11 If You Need Help Command: man (format and display the on-line manual pages) eg. man cp (Read the man page for the cp command) eg. man -k <string> (Search man pages for string) Command: info (Read the info documents) eg. info cp (Read the info document for the cp command) Help associated with the command itself --help or -h parameter (not all commands have this) may display usage 11

12 The File System Unlike Windows, there is a single hierarchical tree (no c:, d: etc) 12

13 The File System The hierarchy is separated by the forward slash character / (not like Windows which uses back slash \) Current directory is a single period:. Directory above is two periods together:.. Previous directory is a hyphen: - Home directory is a tilda: ~ Using the TAB key will auto-complete the file/directory name Hidden files begin with a single period:. 13

14 Introduction to Globbing Globbing allows you to do wildcards saves you time Use * to represent multiple files * on its own is all files/directories *.doc represents all files ending in.doc Use [ and ] to specify groups: [A-Z]*.jpg represents any.jpg file starting with a captial letter Use? as a single character wildcard:?.jpg JPEG files with 1 char names (eg a.jpg, 1.jpg) 14

15 Navigating The File System Command: cd (Change directory) cd /var/tmp (Change to a specific directory) cd.. (Change to the directory above) cd ~/docs (Change to the docs directory in my home) cd (Change to the previous directory) cd www (Change to the bin sub-directory in current path) cd (return to your home directory) 15

16 Navigating The File System Command: ls (list directory contents) ls (show contents in current working directory) ls -la (as above, but show long list, and hidden files) ls -lart (as above, but show in reverse time order) ls /usr/bin (show contents of a specific directory) ls -R (recursively list the current working directory) Command: pwd (Print working Directory): Displays the path of where you are. 16

17 Files & Directories Just like on any other operating system you have normal files and directories (aka: folders) Command: cp (Copy files) cp myfile.doc myfile2.doc (Make a copy of myfile.doc) cp -p myfile.doc myfile2.doc (Same as above but preserve permissions/date stamps etc) cp -r research research2 (Make a copy of directory research) 17

18 Files & Directories Command: rmdir (Remove directory) rmdir mydir (remove the directory mydir - only works if mydir is empty) Command: rm (remove file/directory entries) rm myfile2.doc (remove the file myfile2.doc) Careful with the next command! rm -rf research2 (remove the directory research2 and all it s files & sub-directories) 18

19 Files & Directories Command: mkdir (Make directory) mkdir assignments (make a directory called assignments) mkdir -p mydir/dir1 (make a new directory called mydir/dir1, even if mydir does not exist) 19

20 Symbolic Links Symbolic links point to real files or directories allows you to jump to other files or locations on the file system Command: ln (Make link between files) ln -s myfile_v3.doc myfile_latest.doc (creates a symbolic link called myfile_latest.doc that points to myfile_v3.doc) ln -s /home/demo/dir1/dir2/dir3 /home/demo/jump2dir (creates a symbolic link called jump2dir that points to a deep directory - allows for quicker access) 20

21 File Permissions Linux has Traditional Unix Permissions Also has Access Control Lists very powerful (we won t cover this) Before we talk about permissions, let's look users and groups 21

22 Represented as 9-character code to describe permissions drwxrwx--- 1 dto staff -rw-rw dto staff lrwxr-xr-x 1 dto staff 4096 Nov 26 06:45 my_dir Nov 22 02:12 file_v3.doc 11 Nov 26 16:17 file_latest.doc -> file_v3.doc drwxrwx--- Type Owner Group Other 22

23 File Permissions Octal notation for permissions 0: --- no permission 1: --x execute 2: -w- write 3: -wx write and execute 4: r-- read 5: r-x read and execute 6: rw- read and write 7: rwx read, write and execute 23

24 File Permissions Command: chown (Change ownership) Only root user (administrator) can use this command Command: chgrp (Change group ownership) chgrp staff myfile.doc (Change the group owner to staff) chgrp -R staff docs/ (Recursively change all files and subdirectories under the directory docs) 24

25 File Permissions Command: chmod (change file access permissions) chmod g+rw myfile.doc (Give myfile.doc group read/write permissions) chmod -R g+rw mydir (Recursively give mydir group read/write permissions) chmod 755 mydir (Give mydir group read/execute, other read/execute permissions) 25

26 IO Redirection and Pipes stdin - Standard In (keyboard entry to the command line) Two kinds of screen output stdout - Standard Out (normal screen output) stderr - Standard Error (error output - also to screen output, unbuffered) Pipes - sends stdout to another command use the character eg. cat myfile.txt grep string 26

27 IO Redirection and Pipes Redirection of Input/Output > - Redirect the stdout to a file 2> - Redirect the stderr to a file 2>&1 - Redirect the stderr to stdout < - Use contents of file as keyboard input 27

28 Differences Between Windows and UNIX Text Files Windows and UNIX (Linux, Mac OS X & others) have a different way of representing newlines A newline is known as a line break or end-of-line (EOL) character Windows uses CR+LF (Carriage return + Line Feed) Unix uses just LF A Unix formatted textfile in Windows will appear all as 1 line A Windows formatted textfile in Unix will have a ^M at the end of each line 28

29 Differences Between Windows and UNIX Text Files You can fix this with the unix2dos and dos2unix commands Command: dos2unix (convert a Windows formatted text file to Unix format) dos2unix myfile.txt myfile.txt (will over write the existing file) dos2unix myfile.txt myfile2.txt (will create a new file) Command: unix2dos (convert a Unix formatted text file to Windows format) unix2dos myfile.txt myfile.txt unix2dos myfile.txt myfile2.txt (will create a new file) 29

30 Viewing Text Files Command: cat (concatenate files and print on the standard output) This command will print n number of text files to the screen cat myfile1.txt (print the contents of myfile1.txt to the screen) cat myfile1.txt myfile2.txt (print the contents of myfile1.txt and myfile2.txt to the screen) cat myfile1.txt myfile2.txt > newfile.txt (creates newfile.txt which has the concatenated contents of myfile1.txt and myfile2.txt) 30

31 Viewing Text Files: Pagers Command: more (file perusal filter for crt viewing) more myfile1.txt (print the contents of myfile1.txt but allows the user to scroll down- hit space to scroll, q to quit) Command: less (like more, but allows reverse scrolling) less myfile1.txt (print the contents of myfile1.txt but allows the user to scroll up and down - hit space to scroll down a page, q to quit, arrow up/down to scroll lines) 31

32 Viewing Text Files Command: head (output the first part of a file) head myfile.txt (print the first 10 lines of myfile.txt) head -100 myfile.txt (print the first 100 lines of myfile.txt) Command: tail (output the last part of a file) tail myfile.txt (print the last 10 lines of myfile.txt) tail -100 myfile.txt (print the last 100 lines of myfile.txt) tail -f myfile.txt (follow a file myfile.txt - this will print more as the file is being updated - great for watching log files) 32

33 Text Editors There are three main text editors: pico, including nano. Easy to use but not overly functional emacs, including jove. Relatively easy to use and more feature rich vi, including vim. Complicated but very powerful 33

34 pico & nano Command: nano : These are the very basics nano myfile.txt (open an existing or create a new file called myfile.txt) You can move your cursor around the screen using the arrow keys Just type to enter text To save the file, type: CTRL-O To quit, type: CTRL-X 34

35 emacs & jove Command: emacs : These are the very basics emacs myfile.txt (open an existing or create a new file called myfile.txt) You can move your cursor around the screen using the arrow keys Just type to enter text To save the file, type: CTRL-X, s To quit, type: CTRL-X, CTRL-C 35

36 vi & vim Command: vi : These are the very basics vi myfile.txt (open an existing or create a new file called myfile.txt) You can move your cursor around the screen using the arrow keys To Insert text press i, and type your text. Press esc when finished. To delete a line, type d, d. To save (write) the file, type :, w, [Enter] To quit type :, q, [Enter] 36

37 Transferring Data The terms upload and download are relative to the location. Upload => export, Download => import Many tools used for file transfer ftp old but reliable insecure scp/sftp relatively new, secure (encrypted) rsync only transfers files which have changed (can be very fast) can be encypted using ssh 37

38 ftp Command: open : open a connection to a remote server bin : change to binary mode (you need this when transferring files which aren t text) hash : Toggle # progress bar prompt : Toggle interactive mode (on by default) get <filename> : Download the chosen file mget <filenames> : Download multiple file names (you can use wild cards too) 38

39 ftp Command: ftp $ ftp ftp> o (to) ftp.1000genomes.ebi.ac.uk Connected to ftp.1000genomes.ebi.ac.uk ftp.1000genomes.ebi.ac.uk FTP server 220 Name (ftp.1000genomes.ebi.ac.uk:dto): ftp 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd vol1/ftp/data/na12828/alignment/ 250 Directory successfully changed. ftp> bin 200 Switching to Binary mode. ftp> hash Hash mark printing on (1024 bytes/hash mark). ftp> prompt Interactive mode off. ftp> get NA12828.chrom1.ILLUMINA.bwa.CEU.exon_targetted bam.bai local: NA12828.chrom1.ILLUMINA.bwa.CEU.exon_targetted bam.bai remote: NA12828.chrom1.ILLUMINA.bwa.CEU.exon_targetted bam.bai 227 Entering Passive Mode (193,62,197,91,136,227) 150 Opening BINARY mode data connection for NA12828.chrom1.ILLUMINA.bwa.CEU.exon_targetted bam.bai ( bytes). ################################################################################################# 226 File send OK bytes received in 0.7 seconds (6.9e+02 Kbytes/s) ftp> quit 221 Goodbye. 39

40 scp Part of the OpenSSH suite Command scp - secure copy (remote file copy program) Copy a local file to a remote server $ scp PDL-Stats tar.gz dto@upload.brc.iop.kcl.ac.uk:/tmp dto@upload.brc.iop.kcl.ac.uk's password: PDL-Stats tar.gz 100% 54KB 53.5KB/s 00:00 Copy a remote file to the local server $ scp dto@upload.brc.iop.kcl.ac.uk:/tmp/pdl-stats tar.gz. dto@upload.brc.iop.kcl.ac.uk's password: PDL-Stats tar.gz 100% 54KB 53.5KB/s 00:00 40

41 sftp Part of the OpenSSH suite $ sftp dto@upload.brc.iop.kcl.ac.uk Connecting to upload.brc.iop.kcl.ac.uk... dto@upload.brc.iop.kcl.ac.uk's password: sftp> get local-lib tar.gz Fetching /home/dto/local-lib tar.gz to locallib tar.gz /home/dto/local-lib tar.gz 100% 34KB 34.5KB/s 00:00 sftp> put PDL-Stats tar.gz Uploading PDL-Stats tar.gz to /home/dto/pdl-stats tar.gz PDL-Stats tar.gz 100% 54KB 53.5KB/s 00:00 sftp> quit 41

42 Processes Every program/command you run is a process You can view and stop any of your own processes Command: top (Display Linux tasks) top - 21:04:05 up 16 days, 1:38, 2 users, load average: 3.15, 3.22, 3.24 Tasks: 334 total, 1 running, 332 sleeping, 0 stopped, 1 zombie Cpu(s): 0.1%us, 0.3%sy, 0.0%ni, 97.4%id, 2.1%wa, 0.0%hi, 0.1%si, 0.0%st Mem: k total, k used, k free, k buffers Swap: k total, 176k used, k free, k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND root S :38.56 du 3999 nobody m S :51.41 gmetad root R :00.04 top 779 root S :23.97 pdflush 4528 sge m 16m 5348 S :58.76 sge_qmaster 5619 root S :04.14 kpanfs_thpool 5622 root S :08.67 kpanfs_thpool root m 132m 808 D :26.21 rsync 1 root S :01.59 init 2 root RT S :07.73 migration/0 3 root S :00.26 ksoftirqd/0 4 root RT S :00.00 watchdog/0 5 root RT S :05.62 migration/1 6 root S :00.03 ksoftirqd/1 7 root RT S :00.00 watchdog/1 42

43 Processes Command: ps (report a snapshot of the current processes) ps (show your running processes, short listing) ps -f (show your running processes, full listing) ps -ef (show all processes, full listing) ps -fu dto (show the processes the user dto is running) 43

44 Processes Some times you want to stop a process which isn't responding You first need to know the process number: use the ps command Command: kill (terminate a process) kill (Sends the TERM signal process 12345) kill (Sends the KILL signal process use only if the above fails - doesn t let the process fail gracefully) kill -9-1 (Kills everything you are running. Be careful!) 44

45 Summary The linux command line is very powerful, but there can be a steep learning curve You should now be able to: Log onto a remote linux server Navigate the file system and modify directory structures Change permissions of files/directories View and edit text files & upload/download files View and manage processes 45

46 Questions? Contact me: Skype: brc-mh_linux_support Web: Web: 46

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