Hdi2u intro
Contents
Course schedule
- 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
Course website: http://stab.st-andrews.ac.uk/hdi2u/
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.
Linux particularities
- Connected to Open source code (GNU)
- A grassroots movement
- Immense information out on the web
Unix and Genomics: Common ground
Challenges
- A few large files, multitude of small files
- Small inefficiencies add up to large delays
Strengths
- Automation
- Small, gradual improvements
- Focus on performance
Represents a style of work
Characteristics
- 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 |
|---|---|
| Personal | Shared |
| Single load | Batch load |
| General usage | Focused usage |
| WYSIWYG | WYSIWYM |
The command line (also called the shell) is Unix’s central tool
Unix Philosophy
Aspects
- 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
Measures
- Test before executing
- Realise that the tiniest of details can be important
- Consulting help documentation continuously
