- 1 Course schedule
- 2 Connecting to a remote Machine
- 3 Unix nearly 50 years old
- 4 Why so many different Unix’s?
- 5 Unix and Genomics: Common ground
- 6 Represents a style of work
- 7 Things to get used to
- 8 Unix Philosophy
- This is a cut-down version of 1 day course.
- History and theory has been left out
- Scripting is excluded (although plenty of one-liners)
- Maximise practical aspect.
- Having said that, if you fall behind, listening is better than catching up
Connecting to a remote Machine
Presenting this before introduction as some people might experience delays logging in.
- We shall use a remote machine not the machine you are logged into locally
- The program we shall use is PuTTY.
- Please try to locate PuTTY in the applications section or on AppsAnywhere
Configuring PuTTY for connection
- Server: marvin.st-andrews.ac.uk
- Terminal | keyboard | check VT100+
- Window | Selection | Control use of Mouse | set xterm
- Connect | Data | enter username
- Connection | ssh | X11 Forwarding | Check yes
- Back to PuTTY main screen | select Default setting |click save
You should now be able to open a session, entering your password and get connected to marvin.
Unix nearly 50 years old
- Inspired by CTSS timesharing systems 1964
- Computers were much slower then …but there was alot less data too
- Computers now much faster …but still fall short in meeting big data challenges
Why so many different Unix’s?
- AIX, IBM’s Unix
- HP-UX, HP’s Unix
- Solaris, Sun’s (Oracle’s) Unix
- Linux: Ubuntu, Debian, RedHat, SuSE, many others.
- Mac OSX: s an Unix “under the hood”
- On Windows, you can use Cygwin or install a virtual Linux.
- Connected to Open source code (GNU)
- A grassroots movement
- Immense information out on the web
Unix and Genomics: Common ground
- A few large files, multitude of small files
- Small inefficiencies add up to large delays
- Small, gradual improvements
- Focus on performance
Represents a style of work
- Small tools, do one thing well
- Combine these as building blocks for larger tasks
- Look out for small inefficiencies: they add up to large delays
|Good news||Bad news|
|Details||It’s there somewhere||Demands patience|
|Preparation||Subsequent actions easy||First time is hard|
|Memorizing||Repetition strengthens||Reliance on memory|
Things to get used to
|On one hand||On the other hand|
|Single load||Batch load|
|General usage||Focused usage|
The command line (also called the shell) is Unix’s central tool
- Effective use of the command-line
- Single optimised small tools can be used as building blocks
- Exposes and so does not hide, details
- Powerful approach can lead easily-made big mistakes
- Test before executing
- Realise that the tiniest of details can be important
- Consulting help documentation continuously