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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:

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:

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!