Difference between revisions of "User:Pedrobeltrao/Notebook/Structural analysis of phosphorylation sites/Code"

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(Access)
(SVN usage)
Line 38: Line 38:
 
   cd phospho3d
 
   cd phospho3d
 
   svn update
 
   svn update
     ...make your change...
+
 
 +
     ...make your change; e.g. add new file myscript.py...
  
 
   svn add myscript.py
 
   svn add myscript.py
    ...this schedules your new file for addition...
 
  
 
   svn status
 
   svn status
 +
 
     ...check what has changed locally...
 
     ...check what has changed locally...
  

Revision as of 10:06, 26 September 2009

Owwnotebook icon.png 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:

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

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

Example:

 cd phospho3d
 svn update
   ...make your change; e.g. add new file myscript.py...
 svn add myscript.py
 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'