COMS 6100 Class Notes 3

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1 COMS 6100 Class Notes 3 Daniel Solus September 1, General Remarks The class was split into two main sections. We finished our introduction to Linux commands by reviewing Linux commands I and II and completing Linux commands III and IV. Dr. Carroll emphasized the importance of memorizing these basic commands and using them to become fluent in the language of Linux. The second half of class focused on introducing BASH scripting by previewing several simple examples and introducing possible uses for simple scripts in research and day to day operations. We can see that simple Bash scripts will become increasingly useful as the size of our computational projects grow. I have tried to structure the notes with the information from each slide on the right with instructor comments, questions and discussion on the left. My hope is to provide a review of the discussion during each slide but maybe a summary of each section will be more appropriate. 2 Linux Commands To begin, we used some time to review the basic Linux commands from last class. There was no quiz this time, but these commands represent the foundation of navigation in a Linux environment. There were several interesting questions raised during the discussion of Linux Commands III. Sometimes these questions referred to subtle moves Dr. Carroll used while navigating his personal system. The class seemed to appreciate the ability to quickly reference files and combine commands using shortcuts. Although, sometimes basic commands needed to be covered before a complete explanation could be provided. We spent a great deal of time reviewing Linux IV commands and corresponding examples. The command grep was the focus of some discussion. Dr. Carroll showed the class how he often uses this command to quickly find key information over many large files. 1

2 Combining grep with the > infile and < outfile commands can be very useful for extracting patterns from files and storing them in a new or existing file. Linux Commands I (review) man - show manual for command - show manual for a command, example: man ls (press q to exit the man page) ls - list directory, similar to dir on windows, example: ls /etc, use ls -l /etc to see more detail Notes this is review of Linux Commands I you should know these by heart like a language, you need to become familiar by using these commands cd - change directory, example: cd /etc/ touch - update the timestamp on a file, example: touchfoobar cp - copy a file or directory, example: cp source dest if you want to copy a directory use the -R option for recursive: cp -R /source /dest mv - move a file, example: mv source dest rm - remove a file, example: rm somefile to remove a directory you may need the -R option, you can also use the -f option which tells it not to con rm each file: rm -Rf dir/ mkdir - make a directory, example: mkdir foobar rmdir - remove an empty directory, example: rmdir foobar 2

3 Notes Question: fast? How am I typing so Linux Commands II (review) cat - dumps files to the screen with no page breaks more -displays a file with page breaks after the screen fills up less - displays a file on screen tab complete - hitting tab completes a unique string in Unix Question: What does ll do in your system? its an alias short for ls - lh (likes long listing human readable files/directories) pwd - print working directory - lets you know where you are in the directory structure * - a wild card character - represents any string; eg more * will display every file in the directory. up and down arrows - goes to previous command - a short cut to avoid typing long strings! partial - executes the last command with the name that started with the string partial!$ - the last parameter on the previous line which - locate a command 3

4 Notes: instructor comments about commands These are network connectivity commands You can use du in combination with sort. The unix mentality is to create commands that are simple and robust then later combine commands for greater functionality Recall that the english word echo describes the relfection of ones voice. Similarly, echo in unix reflects the command to the output screen Question: You use the du command with sort? How? Linux Commands III (review) ssh - secure shell - log into a remote computer through the network scp - secure copy - copy a file or files across a network sftp - secure file transfer - transfer files to and from computer through the network du - disk usage - the amount of space files/directories occupy sort - sort lines - alphanumeric or string numeric (with -n) - echo write arguments to the standard output I will show you later. 4

5 Notes: instructor comments about commands IV head is very helpful when you need to preview multiple files quickly man head - to find out more info about the command brackets, [ ] denote options and the pipe is a logical OR head - 10 displays the first 10 lines use head to check format without loading the complete file back ticks get the directory the command was in? grep - you don t know a line but you have a pattern Question: What can you do when you combine the head and tail commands - get middle lines - know the number of the line you re looking for - script to find that one line -simple script to show the head and tail of multiple files (teaser into BASH scripting) Linux Commands IV head - display the first lines of a file tail - display the last lines of a file grep - print lines matching a pattern history - display entered commands > outfile - directs the output of a command to a file named outfile < infile - directs the input of a command from a file named infile 5

6 Notes: instructor comments about commands IV (pipe) - this command takes output and gives it to the following statement ex - history grep > - instead of writing output to the screen save to a file ex - > filename.txt < - infile, take contents and give it as input ex - < filename.txt Example: working example of using infile command - You re a professor that has 100 students all completing the same assignment - writing a program to convert temperature from F to C - I m not typing the same value 100 times! -create a test case to satisfy the input prompt using infile Linux Commands IV head - display the first lines of a file tail - display the last lines of a file grep - print lines matching a pattern history - display entered commands > outfile - directs the output of a command to a file named outfile < infile - directs the input of a command from a file named infile Note: These commands allow you to successfully naviagte any Linux machine. So you must know them. Practice! 6

7 Notes: Explaining Linux IV examples give (grep) a pattern and the command pulls out each line with that pattern grep is very useful in automation, checking to see if something exists quickly Example: A database with two columns (key, value) for a gene family and sequence -we want the name of the gene family -so we grep on the family name -grep HUMAN gets every line with HUMAN in it. Question: Why did you use quotes when using grep that time? - bash will ignore (*) and only references grep - without quotes BASH looks for all files starting with CL71 - with quotes it (grep) looks for the regex in the specified file. Linux Commands IV (Examples) head linuxcommands3.tex head -n 2 linuxcommands3.tex tail linux Commands3.tex grep includegraphics */*.tex history history 11 7

8 Notes: Explaining Linux IV examples history last five hundred and fifty three commands history - In research it is often useful to save the commands used during operation in order to reproduce results for a paper, advisor, or yourself later on! - this command is called bang, not an exclamation point in Unix ctrl c - to cancel an operation /tmp - linux directory for temporary files instead of removing a file just mv the file to the /tmp directory Linux Commands IV (Examples) head linuxcommands3.tex head -n 2 linuxcommands3.tex tail linux Commands3.tex grep includegraphics */*.tex history history 11 Questions? Be sure to review these commands. Try them out and become familiar so we wont need a quiz. 8

9 3 BASH scripting We started by reviewing a few examples of shell scripts and covering some Bash background. These are files with. sh extensions. Previewing these examples we noticed several familiar commands that we just reviewed. Bash configuration files were also covered. Dr. Carroll emphasized that he primarily used one Bash config. file to setup his workspace. We spent significant time discussing variables, which are denoted with the $variable symbol. Understanding how to assign variables and reference them is critical to structuring Bash scripts. Notes: instructor comments about background There was a CLI called shell but they made a new one. Notes: instructor comments about shell script examples in remove firstlines.sh we recognize the command echo code2html - for uploading presentations to the web we run the code through emacs to produce color coordinated HTML jobsmanager.sh - lots of comments, variables, and functions. Shell Scripting BASH: Background Shell Scripting: A shell provides a Command Line Interface (CLI) to interact with the system (especially the file system) BASH GNU Bourne Again SHell Most common shell Shell Script: Examples removefirstlines.sh code2html.sh jobsmanager.sh 9

10 Shell Scripting BASH: Background In HOME directory: Notes: instructor comments about BASH config. files I only really use.bashrc but I suppose I should use.bash profile? I never use.bash logout Files are located in the home directory ls -a shows hidden files Notes: instructor comments about variables Think of variables as buckets when you want to use a variable we use a $ ex. What is in the bucket? -$variable.bash profile: read and executed by Bash every time you log into the system.bashrc: read and executed by Bash every time you start a subshell.bash logout: read and executed by Bash every time a login shell exits if they re missing, Bash defaults to /etc/profile. BASH: Variables Variable names can comprise letters numbers and some characters (, etc.) No data type Assign values to a variable with = and the variable name without a $ Use the variable with a $ 10

11 Bash Variables: Examples Notes: instructor comments about BASH Variables: Examples This is the number 9 not the character 9 These examples illustrate the idea of assigning and referencing variables. Example: 1. STR = Hello World! 2. echo $STR Output: Hello World! Example: Variables as buckets anal- Note: ogy 1. STR= Hello World! 2. echo STR Say you have a bucket You have a hammer next to the bucket You put the hammer in the bucket You add a nailgun to the bucket You now have a nailgun and a hammer in the bucket You take out the nailgun and the hammer then add a screwdriver to the bucket The point is the bucket references the item or items assigned to it. Output: STR Example: 1. COUNTER 2. echo $COUNTER Output: 9 Concatentation: 1. str= Column 1 2. str= $str Column 2 3. str= $str Column 3 4. Header: $str Output: Header: Column 1 Column 2 Column 3 11

12 3.1 Bash: Special Shell Variables These commands are special variables that Bash understands and executes when called. You will never need more than 9 positional parameters, but you can use ${number} to get numbers greater than nine. To echo one of these commands or simply the dollar sign we escape using a forward slash. The return value command $? is usefull when you need to know if the last command executed successfully. The $$ command can provide sudo random numbers. Variable Meaning $0 Filename of script $1 - $9 Positional parameter #1 - #9 ${10} Positional parameter #10 $# Number of positional parameters $* All positional parameters (as a single word) * All positional parameters (as separate strings) $? Return value $$ Process ID (PID) of script $- Flags passed to script (using set) $ Last argument of previous command $! Process ID (PID) of last job run in background 12

13 3.2 Bash: Comments and Conditionals Comments give readers and writers of code a chance to understand and preceive the motivation behind creating variables, functions and operations. Code written with-out comments is insanely difficult to decipher. We should always begin a project by creating an outline of comments first. Then breaking the comments into sections that can be coded independently and later combined to produce a project. No one enjoys writing long papers. We are less likely to discard large sections of code if we begin with an outline. The Robert Frost quote, about coming to a fork in the road, was used to motivate the use of conditionals in code. Much like a fork in the road, where a human can only pick one track, conditionals limit the computer to one track. This method allows us to control the flow of a computer program if a statement is true or false. Bash: Comments Bash ignores everything on a line after a # # s in quotes are not comments Why would we want to put comments in code? So a human can read it! Bash: Conditionals How to tell a computer to do one thing or another Basic form: If expression then statement if expression evaluates to TRUE, then execute statement, otherwise skip it Bash: if [ expression ]; then statement; fi Command-line example: if [ 1 ]; then echo Evaluated to true ; fi Output: Evaluated to true Another form: if expression then statement1 else statement2 if expression evaluates to TRUE, then execute statement1, otherwise execute statement2 Command-line example: if [ 1 ]; then echo Evaluated to true ; else echo Evaluated to false ; fi Output: Evaluated to true 13

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