Getting Started with some Requirements

Java

Before starting setting up Neo4j and, later on, the Clinical Knowledge Graph, it is very important that you have Java installed in your machine.

Different versions of a Neo4j database can have different requirements. For example, Neo4j 3.5 versions require Oracle Java 8, while Neo4j 4.0 versions already require Oracle Java 11. When using a new versionof Neo4j, always remember to read the respective Operations Manual, and check for the software requirements.

To check if you already have Java SE Development Kit installed, run java -version in your terminal window. This should print out three lines similar to the following, with possible variation in the version:

java version "1.8.0_171"
Java(TM) SE Runtime Environment (build 1.8.0_171-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.171-b11, mixed mode)

Running /usr/libexec/java_home in the terminal should print out a path like /Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home. Otherwise, please follow the steps below:

  1. Go to https://www.oracle.com/java/technologies/javase-downloads.html and download the version that fits your Neo4j version and OS requirements.
  2. Install the package.
  3. Run /usr/libexec/java_home in the terminal to make sure the Java package has been installed in /Library/Java/JavaVirtualMachines/.

R

Another essential package for the functioning of the Clinical Knowledge Graph is R.

Make sure you have installed R version >= 3.5.2:

$ R --version

And that R is installed in /usr/local/bin/R:

$ which R

To install the neccessary R packages, simply initiate R (terminal or shell) and run:

install.packages('BiocManager')
BiocManager::install()
BiocManager::install(c('AnnotationDbi', 'GO.db', 'preprocessCore', 'impute'))
install.packages(c('flashClust','WGCNA', 'samr'), dependencies=TRUE, repos='http://cran.rstudio.com/')

Note

If you need to install R, follow these tutorial.

Warning

In Mac OS, make sure you have XQuartz installed.

Now that you are all set, you can move on and start with Neo4j.