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Structure-Based Virtual Screening in Spark
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docking-cpp Update README.md Nov 2, 2016
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README.md

Spark-VS

Spark-VS is a Spark-based library for setting up massively parallel Structure-Based Virtual Screening (SBVS) pipelines in Spark.

Table of Contents

Getting started (on local machine)

First, you need to setup a Spark project with maven, this tutorial is a good starting point: www.youtube.com/watch?v=aB4-RD_MMf0

Then, add the following entries into your pom.xml file:

<repositories>
	...
	<repository>
		<id>pele.farmbio.uu.se</id>
		<url>http://pele.farmbio.uu.se/artifactory/libs-snapshot</url>
	</repository>
	...
</repositories>

<dependencies>
	...
	<groupId>se.uu.farmbio</groupId>
		<artifactId>vs</artifactId>
		<version>0.0.1-SNAPSHOT</version>
	</dependency>
	...
</dependencies>

Finally, since OpenEye libraries are used under the hood, you need to own and a OpenEye license in order to run this. Therefore, you need to set a OE_LICENSE environment variable that points to the license, in your system to run the code in this repository.

Import vs.examples project in Scala IDE

  1. File > Import > General > Existing project into workspace
  2. Select vs.example as root directory
  3. Click finish
  4. Wait for the workspace to build (this can take a while) If the IDE asks to include the scala library or compiler in the workspace click No

If you have scala version problems follow this procedure:

  1. Right click on the project foldel in the Package Explorer > Properties > Scala Compiler
  2. Select fixed scala installation 2.10.X
  3. Click apply and let the IDE clean the project

Now you can get familiar with Spark-VS giving a look to the examples, and running them in Scala IDE. In the data directory you can find an exaple SDF and SMILES files, as well as a receptor file. Remember that in order to run examples you need to specify arguments and OE_LICENSE environment variable through Run Configurations. Later on you may want to create your own project to write specific pipelines for your use case.

Deploy on a Spark cluster

Prerequisites

  • A Spark cluster up and running
    • AWS and GCE offer convenient tools to get this
    • For OpenStack you can use SparkNow
  • An OpenEye Toolkits licese needs to be available on each node of the cluster

Deploy a pipeline

You can start by trying out this pipeline in the examples: Docker.scala. This pipeline takes a receptor (available in the machine that runs the driver) and a SDF library (available in HDFS) as input, and it writes on HDFS the the top N scoring hits.

We provide a JAR with the compiled examples and dependencies: download.

spark-submit --class se.uu.farmbio.vs.examples.Docker \
--master spark://spark-master \
vs.examples-0.0.1-jar-with-dependencies.jar \
--oeLicensePath oe_license.txt \ 
--topN 30 \
hdfs://input.sdf 
receptor.oeb 
hdfs://top30.sdf

If you want to run your custom pipeline, please give a look at the examples and make a new JAR to deploy.

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