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Unix for Bioinformaticians A survival guide Paolo Marcatili - Programmazione 08-09
Agenda ,[object Object],[object Object],[object Object],[object Object],[object Object],Paolo Marcatili - Programmazione 08-09
Unix He can smell your fear Paolo Marcatili - Programmazione 08-09
What is  Unix ? Unix Paolo Marcatili - Programmazione 08-09
What is  Unix ? Unix Paolo Marcatili - Programmazione 08-09
What is  Unix ? Unix Paolo Marcatili - Programmazione 08-09
What is  Unix ? Unix Paolo Marcatili - Programmazione 08-09
What is  Unix ? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Unix Paolo Marcatili - Programmazione 08-09
Types of Unix ,[object Object],[object Object],[object Object],Unix Paolo Marcatili - Programmazione 08-09
Unix Operating System Unix Paolo Marcatili - Programmazione 08-09
What’s in Unix? ,[object Object],[object Object],Unix Paolo Marcatili - Programmazione 08-09
Unix Filesystem Unix Paolo Marcatili - Programmazione 08-09
Terminal ,[object Object],[object Object],[object Object],[object Object],Unix Paolo Marcatili - Programmazione 08-09
Our Task Today Yes, I can! Paolo Marcatili - Programmazione 08-09
Human Immunoglobulins Task Paolo Marcatili - Programmazione 08-09
Human Immunoglobulins Task Paolo Marcatili - Programmazione 08-09
The data ,[object Object],[object Object],[object Object],[object Object],[object Object],Task Paolo Marcatili - Programmazione 08-09
The Task ,[object Object],[object Object],[object Object],[object Object],Task Paolo Marcatili - Programmazione 08-09
Folders: read and write Paolo Marcatili - Programmazione 08-09
Change Directory ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Folders Paolo Marcatili - Programmazione 08-09
Folder content ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Folders Paolo Marcatili - Programmazione 08-09
Wildcards ,[object Object],[object Object],[object Object],[object Object],[object Object],Folders Paolo Marcatili - Programmazione 08-09
Commands ,[object Object],[object Object],[object Object],[object Object],[object Object],Folders Paolo Marcatili - Programmazione 08-09
Unix Permissions Folders Paolo Marcatili - Programmazione 08-09
Folders - summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Folders Paolo Marcatili - Programmazione 08-09
Files: read and write Paolo Marcatili - Programmazione 08-09
Backup original data ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Read a file ,[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Read a file ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Look for text ,[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Edit a file ,[object Object],[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Look for text ,[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Look for text ,[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Grep ,[object Object],[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Grep ,[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Files: sumary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Files Paolo Marcatili - Programmazione 08-09
Processes Paolo Marcatili - Programmazione 08-09
Run a process ,[object Object],[object Object],[object Object],[object Object],[object Object],Processes Paolo Marcatili - Programmazione 08-09
Run - It’s simple ,[object Object],[object Object],Processes Paolo Marcatili - Programmazione 08-09
Run - It’s simple ,[object Object],[object Object],[object Object],Processes Paolo Marcatili - Programmazione 08-09
Controlling processes ,[object Object],[object Object],[object Object],[object Object],[object Object],Processes Paolo Marcatili - Programmazione 08-09
Controlling processes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Processes Paolo Marcatili - Programmazione 08-09
Redirection Control the force Paolo Marcatili - Programmazione 08-09
Inputs and outputs Keyboard Mouse Tablet Kernel Display Printer File Redirection Paolo Marcatili - Programmazione 08-09
Write into a file ,[object Object],[object Object],[object Object],[object Object],[object Object],Redirection Paolo Marcatili - Programmazione 08-09
Append to a file ,[object Object],[object Object],[object Object],[object Object],[object Object],Redirection Paolo Marcatili - Programmazione 08-09
The big one! ,[object Object],[object Object],[object Object],[object Object],Redirection Paolo Marcatili - Programmazione 08-09
Extract headers ,[object Object],[object Object],[object Object],Redirection Paolo Marcatili - Programmazione 08-09
Extract headers ,[object Object],[object Object],[object Object],[object Object],[object Object],Redirection Paolo Marcatili - Programmazione 08-09
Redirect everything! ,[object Object],[object Object],Redirection Paolo Marcatili - Programmazione 08-09
Redirect - summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Redirection Paolo Marcatili - Programmazione 08-09
Quiz ,[object Object],[object Object],[object Object],[object Object],[object Object],Paolo Marcatili - Programmazione 08-09

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Unix Master