A Graph database for Galaxy tools

Setting up Neo4j

General neo4j reference:

https://neo4j.com/docs/developer-manual/3.2/introduction/

Fast way using docker

1. docker pull neo4j

2. Create folder structure for storing neo4j database content, import data, and logs outside the docker container:

   cd $HOME &&
   mkdir neo4j neo4j/data neo4j/import neo4j/logs
   

3. Launch neo4j

   The command below will

   • make neo4j accessible via its http (port 7474) and bolt interfaces (port 7687)
   • make it store database data and logs in mapped locations outside the container and
   • look for import data in an external folder, too
   • have it act on behalf of the current user (so that you have regular access rights to the data in the mapped locations)

   sudo docker run \
   --publish=7474:7474 --publish=7687:7687 \
   --volume=$HOME/neo4j/data:/data --volume=$HOME/neo4j/import:/import --volume=$HOME/neo4j/logs:/logs \
   --user=`id -u`:`id -g` neo4j
   

4. Check availability of the database server in your browser at http://127.0.0.1:7474/browser/

Resources:

• https://neo4j.com/docs/operations-manual/current/docker/
• https://neo4j.com/developer/docker-run-neo4j/
• https://neo4j.com/developer/docker/

Installation using OS package manager (Ubuntu):

1. Install java and check version

   • sudo apt install default-jre
   • java --version

2. Install Neo4j

   • 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=1:3.5.12

3. Minimal configuration of neo4j

   • Uncomment the line dbms.connectors.default_listen_address=0.0.0.0 in /etc/neo4j/neo4j.conf

4. Starting/Stopping the Neo4j database service

   • sudo service neo4j start
   • sudo service neo4j stop
   • sudo service neo4j restart

Resources:

• https://neo4j.com/docs/operations-manual/current/installation/linux/debian/#debian-installation
• https://dzone.com/articles/installing-neo4j-on-ubuntu-1604

Use neo4j Desktop

https://neo4j.com/download/neo4j-desktop/?edition=desktop

Installation of Python requirements

Using Python3 venv

1. python3 -m venv graph_db
2. . graph_db/bin/activate
3. pip install py2neo requests

Using conda

1. conda create --name graph_db python=3.6
2. pip install py2neo
3. conda install requests

Building the graph database

Copy data files to neo4j import directory

• For a OS package manager installed neo4j:

  sudo cp data/* /var/lib/neo4j/import/

• For neo4j running in docker:

  cp data/* $HOME/neo4j/import

First connection to the database server

1. Visit http://127.0.0.1:7474/browser/ in your browser and log in with the default credentials:

   username: neo4j
   password: neo4j
   

2. Set a new password upon being prompted to do so

Import the data

Find the file run_create_db.sh inside the cloned repo folder, and:

1. Edit it to use

   • the password you set for your database account
   • the paths to the CSV data files in the neo4j import directory (see above)

2. From inside the cloned repo folder run:

   sh run_create_db.sh

Building the database should take < 1 minute with an OS package manager-installed neo4j (expect 1-5 minutes with the less performant docker version).

After that go back to the neo4j web interface and start exploring!