SetupBallaxyInstance

Create your ballaxy instance

If you want to set up your own instance of ballaxy, you just have to follow these steps:

1.) Create a new folder called ballaxy in your home directory (or somewhere else) and enter it.
2.) Clone the ball repository with the command git clone https://bitbucket.org/ball/ball in this new folder. Optionally you can also use SSH to do so.
3.) Clone the galaxy repository with the command hg clone https://bitbucket.org/galaxy/galaxy-dist/`
4.) Enter the galaxy repository with "cd galaxy-dist" and update it with hg update stable
5.) Enter the ball repository with "cd ball" from the ballaxy folder and create a new folder called build with mkdir build
6.) Enter the new folder with cd build and configure ball by typing cmake .. -DBALL_BUILD_BALLAXY=true
7.) Compile ballaxy by typing make ballaxy in the same folder
8.) Enter the folder "tools" in the galaxy repository and create a symlink called "BALL" to the folder /home/username/ball/build/ballaxy/default/config by typing "ln -s /home/username/ballaxy/ball/build/ballaxy/default/config/ BALL"
9.) After doing this, you have to copy the configuration of the ballaxy build located in the file tool_conf.xml.section in the folder /~/ballaxy/ball/build/ballaxy/default to the right destination. You can do this by opening the file tool_conf.xml.section in /~/ballaxy/galaxy-dist, removing all sections parts, entering the content of the file mentioned before and saving the result as "tool_conf.xml". The result should look similar to the following:

<?xml version="1.0"?>
<toolbox>
 	<section name="Preparation" id="Preparation">
		<tool file="BALL/PropertyModifier.xml"/>
		<tool file="BALL/LigandFileSplitter.xml"/>
		<tool file="BALL/PeptideBuilder.xml"/>
		<tool file="BALL/EvenSplit.xml"/>
		<tool file="BALL/BindingDBCleaner.xml"/>
		<tool file="BALL/PartialChargesCopy.xml"/>
		<tool file="BALL/PDBCutter.xml"/>
		<tool file="BALL/BondOrderAssigner.xml"/>
		<tool file="BALL/MolFilter.xml"/>
		<tool file="BALL/Split2ConnectedComponents.xml"/>
	</section>

 	<section name="Convert, combine and store" id="Convert, combine and store">
		<tool file="BALL/DBImporter.xml"/>
		<tool file="BALL/Converter.xml"/>
		<tool file="BALL/DockResultMerger.xml"/>
		<tool file="BALL/TrajectoryFile2PDBSplitter.xml"/>
		<tool file="BALL/VendorFinder.xml"/>
		<tool file="BALL/MolCombine.xml"/>
	</section>

 	<section name="Rescoring" id="Rescoring">
		<tool file="BALL/TaGRes.xml"/>
		<tool file="BALL/TaGRes-train.xml"/>
		<tool file="BALL/AntitargetRescorer.xml"/>
		<tool file="BALL/SimpleRescorer.xml"/>
	</section>

 	<section name="Docking" id="Docking">
		<tool file="BALL/SpatialConstraintDefiner.xml"/>
		<tool file="BALL/IMGDock.xml"/>
		<tool file="BALL/GridBuilder.xml"/>
		<tool file="BALL/ConstraintsFinder.xml"/>
		<tool file="BALL/PocketDetector.xml"/>
		<tool file="BALL/DockPoseClustering.xml"/>
		<tool file="BALL/InteractionConstraintDefiner.xml"/>
		<tool file="BALL/WaterFinder.xml"/>
	</section>

 	<section name="Get Data" id="Get Data">
		<tool file="BALL/CombiLibGenerator.xml"/>
		<tool file="BALL/PDBDownload.xml"/>
		<tool file="BALL/DBExporter.xml"/>
	</section>

 	<section name="File conversion" id="File conversion">
		<tool file="BALL/MolecularFileConverter.xml"/>
	</section>

 	<section name="QuEasy (QSAR)" id="QuEasy (QSAR)">
		<tool file="BALL/Predictor.xml"/>
		<tool file="BALL/Validator.xml"/>
		<tool file="BALL/FeatureSelector.xml"/>
		<tool file="BALL/MolPredictor.xml"/>
		<tool file="BALL/ModelCreator.xml"/>
		<tool file="BALL/InputReader.xml"/>
		<tool file="BALL/InputPartitioner.xml"/>
		<tool file="BALL/AutoModel.xml"/>
	</section>

 	<section name="Scoring" id="Scoring">
		<tool file="BALL/SLICK.xml"/>
	</section>

 	<section name="Checks and evaluations" id="Checks and evaluations">
		<tool file="BALL/LigCheck.xml"/>
		<tool file="BALL/ProteinCheck.xml"/>
	</section>

 	<section name="Analysis" id="Analysis">
		<tool file="BALL/PropertyPlotter.xml"/>
		<tool file="BALL/SimilarityAnalyzer.xml"/>
		<tool file="BALL/RMSDCalculator.xml"/>
		<tool file="BALL/ScoreAnalyzer.xml"/>
	</section>

 	<section name="DEFAULT" id="DEFAULT">
		<tool file="BALL/GalaxyConfigGenerator.xml"/>
	</section>

 	<section name="Chemoinformatics" id="Chemoinformatics">
		<tool file="BALL/FingerprintSimilaritySearch.xml"/>
		<tool file="BALL/FingerprintSimilarityClustering.xml"/>
	</section>

 	<section name="Structure Creation" id="Structure Creation">
		<tool file="BALL/CrystalGenerator.xml"/>
	</section>

</toolbox> 

10.) Make sure that all necessary libraries have been included correctly by doing the following: (either in a terminal, which will work temporarily or in the file .bashrc in your home folder, which will work permanently)

export PYTHONPATH=~/ballaxy/ball/build/lib/
export LD_LIBRARY_PATH=~/ballaxy/ball/build/lib/
export BALL_DATA_PATH=~/ballaxy/ball/data/
export PATH=$PATH:~/ballaxy/ball/build/bin/
export PATH=$PATH:~/ballaxy/ball/build/bin/TOOLS/

11.) To start the ballaxy server, just enter sh run.sh in the root folder of the galaxy repository.
12.) If you enter http://127.0.0.1:8080/ in your browser, you should now be able to use ballaxy. Enjoy! :-)