User:Pedrobeltrao/Notebook/Structural analysis of phosphorylation sites/Code: Difference between revisions
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==Access== | ==Access== | ||
1. Install a [http://subversion.tigris.org/ | 1. Install a [http://subversion.tigris.org/ subversion (svn)] client | ||
2. Then check out the latest version of the code: | 2. Then check out the latest version of the code: | ||
<code>svn checkout http://phospho3d.googlecode.com/svn/trunk/ phospho3d | <code>svn checkout http://phospho3d.googlecode.com/svn/trunk/ phospho3d</code> | ||
* This will create a folder phoshpho3d | * This will create a folder "phoshpho3d" in your current directory | ||
* Project members | * 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/ | 3. Before running python scripts, you also need to [http://biskit.pasteur.fr/install/short/ install the Biskit library] | ||
* apart from the core library, the following helper applications will be useful: | * apart from the core library, the following helper applications will be useful: | ||
** [http://biskit.pasteur.fr/install/applications/surfrace surfaceracer] | ** [http://biskit.pasteur.fr/install/applications/surfrace surfaceracer] | ||
** pymol | ** 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 | |||
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:==== | |||
<code> | |||
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 update | |||
svn ci -m 'your checkin message' | |||
</code> | |||
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: | |||
<code> | |||
svn ci myscript.py -m 'new script for annotating domains' | |||
</code> | |||
Latest revision as of 11:23, 26 September 2009
Structural analysis of phosphorylation sites | |
CodeWe are going to use Perl (Pedro) and Python (Raik). The Python code builds on the Biskit library. Our scripts are available through Google Code: Access1. Install a subversion (svn) client 2. Then check out the latest version of the code:
3. Before running python scripts, you also need to install the Biskit library
SVN usageAfter the initial checkout, the basic principle is always:
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:
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:
|