Introduction to Unix

Introduction to Unix ICarolin KosiolInstitute of Population GeneticsVetmeduni ViennaSpezielle Bioinformatik in der BiomedizinSS 2013

Unix: not just an unfortunate name“Hold it right there, buddy”“That scruffy beard… Those suspenders. That smug expression”“You’re one of those condescending unix computer users!”“Here’s a nickel kid. Get yourself a better computer”SourcesDILBERT ©2009, UNITED FEATURE SYNDICATE, INC (Scott Adams)Ken and Dennis: Wikipedia, public domain

Why? It’s cool now …Every Apple computer, the iPhone and most recent iPodshave a Unix base underneath their façade.

But really...why?~ 1KB / day100GB / run~300 million fragmentsMultiplex 96 different samples300GB / run~1.5 billion fragments

File SystemFiles on a Unix system are in a tree structureRoot directory, also called /Top level directoriesKeith’s filespwd/Users/student/unix/# The following refer to the same file. First, absolute filename from the root# A forward slash / separates directory names# cat prints the contents of a file on the screencat /Users/student/unix/haikuA crash reducesyour expensive computerto a simple stone.# File name relative to current location (/Users/student/unix/)cat unix/haiku

File system

Terminal & Command line

whoamistudent1pwd/Users/studentlsDocuments … … unixcd Dcd D cd Decd ..cdGetting from ‘A’ to ‘B’

Move and Copypwd/Users/student/unix/MoveCopylsalignmnet.fasta read-only test testmv alignmnet.fasta alignment.fastalsalignment.fasta read-only test testcp alignment.fasta alignment_copy.fastalsalignment.fasta alignment_copy.fasta read-only test test

Dealing with Multiple Filespwd/Users/student/unix/MultipleFilesmkdir Fasta Treecp *.fasta Fastacp *.tree Tree

Removing files and directoriespwd/Users/student/unix/MoveCopyrm read-onlyrm:rm /dev/nullrm testalignment.fasta read-only test testrmdir testls testafilerm test/afilerm test/afilermdir test

Man pages (Getting help)man lsman cdman man (yes even the man command has a manual page)ls -lls -a

SummaryTheabsolutebasicsBasic file controlViewing/creating/editing filesMisc.usefulcommandsPowercommandsProcessrelatedcommandsls mv less man uniq topcd cp head chmod sort pspwd mkdir tail source cut killrmdir touch wc trrm nano curl grepI (pipe)sed> (write to file)< (read from file)

ExercisesThe exercises are already installed on the institute computersTo install on your own computer, use the following recipe.To download and install exercises# Type commands in bold# Lines starting with hash are comments# Make sure you are in home directorycd# Download file containing exercises (curl) and unpack (tar)curl –L ‘http://tinyurl.com/32a2gbk/unix.tgz’ | tar –zx# List files and make sure everything worked.#You should see a directory called exerciseslsTo remove# Make sure you are in home directorycd# Remove exercises. The directory and everything in it,# including subdirectories, will be deletedrm –rf exercise

Introduction to Unix IICarolin KosiolInstitute of Population GeneticsVetmeduni ViennaNext Generation Sequencing CourseSS 2013

Are we just making life hard for ourselves?Every command• reads text from its standard input (“stdin”)• writes text to standard output (“stdout”)• writes errors to standard error (“stderr”)KeyboardstdinCommandstdoutScreenUse a pipe | to connect the stdout of one command to the stdin of anotherKeyboardCommand 1Command 2ScreenChain commands to perform more complex tasks5 individual commands 25 possible pairs 125 triplets …

UNIX pipespwd/Users/student1/unix/Pipescat transcripts.fasta.gz | gunzipgunzip < transcript.fasta.gz | grep ‘^>’ | cut –d ‘|’ –f|_sort | uniq –c > transcript_counts.txt

First shell scriptpwd/Users/student/unixecho ‘echo $VAR’ > scriot..shVAR=“Hello”chmod +x script.sh./script.shHello

R Language for Statistical Computing> x y print(y) # print (vector) y[1] 1 4 9 16 25 36> mean(y) # Calculate average (arithmetic mean) of (vector) y;# result is scalar[1] 15.16667> var(y) # Calculate sample variance[1] 178.9667> lm_1 print(lm_1) # Print the model from the (linear model object) lm_1q();

Appendix

ThanksforlisteningInstitute of Population Genetics(Univ of Veterinary Medicine Vienna)Tim Massingham(European Bioinformatics Institute)