Introduction to Scripting Workshop October

Introduction Rob Lane & The HPC Support Team Research Computing Services CUIT

Introduction First Intro to Scripting Workshop Thanks for agreeing to be guinea pigs! Please Leave Feedback

Introduction Will be sent out afterwards: Slides Commands cheat sheet

Other Resources Shell and Scripting Tutorial

Other Resources How Linux Works Available at Safari Books Online

Other Resources Advanced Bash-Scripting Guide

Introduction What is a shell script?

Introduction What is a shell script? A file with shell commands.

Access Windows Instructions 1.Search for putty on Columbia home page 2.Select first result 3.Follow link to Putty download page 4.Download putty.exe 5.Run putty.exe

Access Mac Instructions 1.Run terminal

Access Mac (Terminal) $ ssh Windows (Putty) Host Name: didius.cc.columbia.edu

Access Aside System: cunix.columbia.edu User: Your UNI

Workshop Setup $ mkdir workshop $ cd workshop $ cp /tmp/workshop/*.

Command Line Example Word Count from “Data Science at the Command Line” - Jeroen Janssens

wcount $ cat wcount cat alice.txt | tr …

wcount $ wcount

wcount $ wcount -bash: wcount: command not found

wcount $./wcount

wcount $ wcount -bash:./wcount:Permission denied

wcount $ ls –l wcount

wcount $ ls –l wcount -rw-rw---- [ snip ]

wcount $ ls –l wcount -rw-rw---- [ snip ] $ chmod +x wcount

wcount $ ls –l wcount -rw-rw---- [ snip ] $ chmod +x wcount $ ls –l wcount -rwxrwx--x [ snip ]

wcount $./wcount Should work this time.

wcount Choose an editor nano  Recommended default vi emacs

wcount Choose an editor nano  Recommended default vi emacs

nano Nano commands are on back of cheat sheet. ^ means “hold down control”

Edit wcount $ nano wcount

#! Add “#!” to first line #!/bin/sh cat alice.txt | tr …

#! $./wcount Still works.

#! Some #! first lines you might see #!/bin/sh #!/usr/bin/perl #!/usr/bin/python

Variables $ file=alice.txt $ echo $file alice.txt

Variables 1.Add file=alice.txt to wcount. 2.Replace cat alice.txt with the variable.

Variables #!/bin/sh file=alice.txt cat “$file” | tr …

Variables Why put quotes around $file? cat “$file” | tr …

Command Line Parameters Change wcount so any file can be specified from the command line. $./wcount moby.txt

Command Line Parameters Change wcount so any file can be specified from the command line. $./wcount moby.txt  $1

Command Line Parameters 1.Create a new file named “param” 2.Put the #! directive on the first line 3.One bash line: “echo $1” 4.Save and make executable 5.Run it

Command Line Parameters $ cat param #!/bin/sh echo $1

Command Line Parameters $./param $./param alice.txt $./param aaa bbb ccc

Command Line Parameters Update wcount to use $1 instead of alice.txt.

Command Line Parameters Before: file=alice.txt After: file="$1"

Command Line Parameters Update param to print out $# echo $# echo $1 Run it with different numbers of parameters

if if [[ condition ]] then do something fi

[, [[, (( [ : Standard comparison [[ : Extended comparison (( : Mathematical comparison

[, [[, (( [ : Standard comparison [[ : Extended comparison  (( : Mathematical comparison

Comparison with [[ if [[ “$count” -eq 100 ]] -eq : equals -ne : not equal -gt : greater than …etc.

if if [[ $# -ne 1 ]] then do something fi

if if [[ $# -ne 1 ]] then echo “Usage: wcount file” exit 1 fi

if $./wcount $./wcount alice.txt $./wcount alice.txt junk

if if [[ ! –f “$file” ]] then echo “Error: File $file not found.” exit 1 fi

File Tests Common tests -e : File exists -f : File is “regular” -d : File is a directory …many more

if if [[ ! –f “$file” ]] then echo “Error: File $file not found.” exit 1 fi

Add lines parameter Show the five most common words: $./wcount alice.txt 5

while i=7 while (( $i > 4 )) do echo $i i=`expr $i - 1` done

for for i in aa bb cc do echo $i done for file in `ls` do ls $file done

readyourmind A silly impolite script but it shows a few more things. read : read input case : another way to control flow

End of Slides Questions?