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

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Structural analysis of phosphorylation sites
 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Structural analysis of phosphorylation sites


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=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:
 * This will create a folder "phoshpho3d" in your current directory
 * Project members can check out a write-access copy. See: 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:


 * 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)

Example:
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:


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