User:Pedrobeltrao/Notebook/Structural analysis of phosphorylation sites/Code

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Owwnotebook icon.png Structural analysis of phosphorylation sites


We are going to use Perl (Pedro) and Python (Raik). The Python code builds on the Biskit library. Our scripts are available through Google Code:


1. Install a subversion (svn) client

2. Then check out the latest version of the code:

  svn checkout phospho3d

3. Before running python scripts, you also need to install the Biskit library

  • apart from the core library, the following helper applications will be useful:

SVN usage

After the initial checkout, the basic principle is always:

  1. Update your local copy from the code base on the server
  2. Make your change
  3. Update again
  4. Submit (check in) your change to the server

There are many graphical front-ends to subversion and most programming environments integrate some subversion support. But even without any GUI candy, you only need to remember 3 or 4 svn commands to work on the code. These are:

  • svn add -- add a new file/files into version control
  • svn update -- merge changes from the server into your local copy
  • svn checkin (short: svn ci) -- submit changes to the server
  • svn status -- list local changes (option -u lists remote changes too)


 cd phospho3d
 svn update
   ...make your change; e.g. add new file
 svn add
 svn status
   ...check what has changed locally...
 svn update
 svn ci -m 'your checkin message'

Allways update your local copy to the latest state **directly before** checking in any change! By default, svn commands operate on the local folder and all sub-folders. You can limit them to certain files: svn ci -m 'new script for annotating domains'