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

Structural analysis of phosphorylation sites

Code 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: http://code.google.com/p/phospho3d/ Access 1. Install a subversion (svn) client 2. Then check out the latest version of the code: svn checkout http://phospho3d.googlecode.com/svn/trunk/ phospho3d-read-only This will create a folder phoshpho3d-read-only in your current directory Project members should check out a write-access copy. You will find your personal checkout command on the GoogleCode page after signing in: http://code.google.com/p/phospho3d/source/checkout 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: surfaceracer pymol SVN usage After the initial checkout, the basic principle is always: Update your local copy from the code base on the server Make your change Update again Submit (check in) your change to the server Example: cd phospho3d svn update ...make your change... svn add myscript.py ...this schedules your new file for addition... svn status ...check what has changed locally... svn ci -m 'your checkin message' By default, svn commands operate on the local folder and all sub-folders. You can limit them to certain files: svn ci myscript.py -m 'new script for annotating domains'