Rf: Created page with "= 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 pr..."

2017-04-19T21:47:08Z

Created page with "= 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 pr..."

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= 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: <code>http://stab.st-andrews.ac.uk/hdi2u/</code>

= 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

Hdi2u intro - Revision history

Rf: Created page with "= 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 pr..."