Getting Started With Darwin

This page is intended for students that attend exercises in Computational Biology. It explains how to access and use darwin.

Some helpful links:

• Last week's linux/unix tutorial
• The darwin online help

If any of these instructions cause a problem, don't hesitate to ask an assistant. They are there to help you.

Task 1: Setting up Darwin

Starting Darwin in the student computer rooms

Log-in to one of the PC's in CAB H56 under linux. Open a terminal window, and enter the following command:

/home/darwin/bin/darwin

this should bring up the darwin prompt which looks like this:

Darwin: Sequence Searching Facility
Version 4.0, 2008-09-11
  (c) E.T.H. Zurich
>

Now you are ready to type in commands (e.g. from the Introduction to Darwin). Or type "done" to quit the Darwin session.

Creating a shortcut
Always typing the long command with the full path is not very convenient. Linux offers a system for short cuts called alias. If you are using the tcsh shell, add this line to the .tshrc file by using the text editor of your choice (e.g. Gedit in the desktop environment, nano or vim in the terminal):

alias darwin /home/darwin/bin/darwin

If you are using bash, then add this to your .bashrc file

alias darwin="home/darwin/bin/darwin"

Now you can simply type "darwin", independent of your current directory. If you don't know which shell you are using, either just put it in both files (or in those that exist).

Starting Darwin on your private PC or notebook

Darwin is free available and can be obtained from the CBRG homepage. After you get Darwin for your operating system, decompress the file and start darwin with the following command:

darwinfolder/darwin -l darwinfolder/lib

darwinfolder is the path to the darwin executable file. Please take care that with some distributions the executable file is in a separate folder (e.g. /linux). Then you have to type in:

darwinfolder/linux/darwin -l darwinfolder/lib

Now you should be able to type in Darwin commands at the prompt '>'.

Task 2: First Steps in Darwin

To learn the basics of Darwin, work through the Introduction to Darwin. Part of it adresses basic programming, part of it explains Darwin features for the advanced user. You don't have to understand (and remember) everything at this moment, but once you have seen it, you know where to go back to later.

The Darwin Quick Reference can be useful for this task, but also later.

Task 3: Writing your first Darwin Program

Now it is time to try to write your own Darwin programs. Solve the five problems of "6: Some Real Problems (i.e. Self Test)" of the Introduction to Darwin.