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Reactome Setup Guide

The following are the instructions to get Reactome running on Ubuntu 18.04. For other OS, please refer to the official Neo4j documentation.

1. Install Java 8

Neo4j specifically requires Java 8 to be installed. If you don't have Java installed, you can install it with the command below:

$ sudo apt install openjdk-8-jdk

Otherwise validate that you have Java 8 installed:

$ java -version
openjdk version "1.8.0_181"

2. Install Neo4j Community Edition

Linux Installation - Neo4j Reference.

Run the following commands to install Neo4j Community Edition 3.4.6:

$ wget -O - https://debian.neo4j.org/neotechnology.gpg.key | sudo apt-key add -
$ echo 'deb https://debian.neo4j.org/repo stable/' | sudo tee -a /etc/apt/sources.list.d/neo4j.list
$ sudo apt-get update
$ sudo apt-get install neo4j=1:3.4.6

Later version of Neo4j can also be used, as long as it is version 3 (version 4 seems to have problems with Reactome database).

Verify that Neo4j is running:

$ sudo service neo4j status

From the status above, you can see that $NEO4J_HOME is located at /var/lib/neo4j. If Neo4j is not running, start it:

$ sudo service neo4j start

Once it's running, set the initial password to whatever you prefer.

$ curl -H "Content-Type: application/json" -X POST -d '{"password":"WHATEVER THE PASSWORD IS"}' -u neo4j:neo4j http://localhost:7474/user/neo4j/password

3. Install Reactome database

See https://reactome.org/dev/graph-database

Download the Reactome database. Extract and move it to $NEO4J_HOME/data/databases.

$ wget https://reactome.org/download/current/reactome.graphdb.tgz
$ tar xvzf reactome.graphdb.tgz
$ sudo mv graph.db /var/lib/neo4j/data/databases
$ chown -R neo4j:neo4j /var/lib/neo4j/data/databases/graph.db

Edit the config file at either $NEO4J_HOME/conf/neo4j.conf or /etc/neo4j/neo4j.conf. Change dbms.active_database to dbms.active_database=graph.db if necessary.

Check that the neo4j service is running with the following command. If it is not running, start it.

$ sudo service neo4j status

For graph database connection in PALS, be sure to set the following environmental variables:

  • NEO4J_SERVER: your Neo4j server (default: bolt://localhost:7687)
  • NEO4J_USER: your Neo4j user name (default: neo4j)
  • NEO4J_PASSWORD: your Neo4j password (default: neo4j)