Installation and Configuration for SBFC osgi

Introduction
Aside from the standard branch (trunk), SBFC core is also available in a branch, called SBFC osgi using the OSGi package architecture. The OSGi technology offers a substantial support for developing highly modular applications and is a design key for the software Cytoscape, a powerful visualisator and analyser of biological networks. By implementing a SBFC branch adopting OSGi, we hope to make easier to port SBFC into Cytoscape and other software adopting OSGi in the long term.

Requirements
To follow these directions you will need the following tools:
 * Eclipse with the Plug-in Development Environment (PDE) included. As indicated here, the PDE comes with the Classic, Java EE or RCP/Plugin versions of eclipse.
 * A tool for checking out a repository from subversion (e.g. subclipse for Eclipse, Tortoise for Windows, or the typical SVN command line client for Linux and Mac OSX).

Set up for SBFC (OSGi)
This section explains how to set up and configure SBFC (osgi) and Ant (see http://ant.apache.org/).

Check out source code
As reference, SBFC_osgi will be the directory containing the project to check out. Move to the directory where you want to check out the project. You can download SBGC OSGI using one of the following methods:

a) Command line check out with SVN    svn co https://svn.code.sf.net/p/sbfc/code/branches/osgi SBFC_osgi

b) Eclipse. Check out source code with subclipse SVN (see http://subclipse.tigris.org):    File -> Import -> SVN -> Checkout Projects with SVN      URL= svn://svn.code.sf.net/p/sbfc/code/branches/osgi     Create new Java Project -> Save the project as SBFC_osgi -> Finish

After checking out the project, you will need reference the SBFC_osgi libraries to the Java Build Path. In Eclipse: Package Explorer -> SBFC_osgi -> Properties -> Java Build Path -> Add JARs Expand SBFC_osgi -> Expand lib. Select all the jar files in lib -> OK.

Set up and configure SBFC (OSGi) with Ant
a) Eclipse:  (Set up)   Package Explorer window -> open the project SBFC_osgi;   Select build.xml -> Run As -> External Tools Configurations;   In the window corresponding to SBFC_osgi build.xml, select osgi in the tab Targets.   (Run)   Package Explorer window  -> open the project SBFC_osgi;   Select build.xml -> Run As -> Ant Build. b) Run using command line: cd SBFC_osgi ant osgi

??? Set up target platform What is this section about?
a) for Linux and Windows users:   Window -> Preferences -> Plug-in Development (expand!) -> Target Platform -> Add ->     Nothing: Start with empty target platform -> (in the new window) click on Add -> Directory -> Browse ->    Select the folder lib-bundles/ in the sbfc directory -> Finish -> Apply -> Ok

b) for Mac OSX users:   Eclipse -> Preferences -> Plug-in Development -> Target Platform -> Running Platform -> Edit ->   (in the new window) click on Add -> Directory -> Browse -> lib-bundles/ directory in the sbfc directory -> OK

Make sure that the new target platform is now selected.

??? Import projects What is this section about?
(a) Fast way (only works in Eclipse):

* unzip metadata.zip file in sbfc directory * in Eclipse: File -> Import -> General (Expand!) -> Existing Projects into workspace -> Next Select Root Directory -> Browse -> Select sbfc directory Select All (or only the ones you want to use) -> Finish

(b) Slow way:

* TODO!

Run SBFC OSGi
If the building process was successful, run SBFC with the required command line arguments (e.g.). The options -converter and -inputfile are required for every converter: ./sbfc.sh -converter sbml2biopax2 -inputfile ~/modelfile.xml

For information how to use the command line tool: ./sbfc.sh help

If you want to have a list of all available registered converters, please use the following command (also shows which arguments are required for a converter): ./sbfc.sh converters