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

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(SVN usage)
(Access)
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2. Then check out the latest version of the code:
2. Then check out the latest version of the code:
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   <code>svn checkout http://phospho3d.googlecode.com/svn/trunk/ phospho3d-read-only</code>
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   <code>svn checkout http://phospho3d.googlecode.com/svn/trunk/ phospho3d</code>
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* This will create a folder phoshpho3d-read-only in your current directory
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* This will create a folder "phoshpho3d" in your current directory
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* 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
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* 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 [http://biskit.pasteur.fr/install/short/ install the Biskit library]
3. Before running python scripts, you also need to [http://biskit.pasteur.fr/install/short/ install the Biskit library]
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** [http://biskit.pasteur.fr/install/applications/surfrace surfaceracer]
** [http://biskit.pasteur.fr/install/applications/surfrace surfaceracer]
** pymol
** pymol
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==SVN usage==
==SVN usage==

Revision as of 13:05, 26 September 2009

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...
 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'


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