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Clone Git Repository

    git clone git@github.com:BackofenLab/protein-graph-database.git
    cd protein-graph-database/

Install Neo4j on Mac

0. Install Homebrew

    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
	brew doctor # to check if homebrew is working

1. Install java version 11 with brew

brew install openjdk@11

2. Download Neo4J 4.4.20 (LTS) - Community Edition

https://neo4j.com/download-center/#community

3. Extract the tar file

4. Save Neo4J where you want it to be

<NEO4J-HOME> := <Path-To-Neo4j-parent-directory>/neo4j/

5. Check for multiple java versions

/usr/libexec/java_home -V

6a. (Change java version to 11)

    export JAVA_HOME=`/usr/libexec/java_home -v <JAVA-VERSION>`

6b. (Change default java version in bash)

  • Open ~/.bashrc
  • add this line:
    export JAVA_HOME=$(/usr/libexec/java_home -v <JAVA-VERSION>)
  • Save and exit TODO: Change default version to 11

7. Install APOC Plugin

curl https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/4.4.0.1/apoc-4.4.0.1-all.jar -o <NEO4J-HOME>/plugins/apoc-4.4.0.1-all.jar

8. Check if Neo4j runs

<NEO4J-HOME>/bin/neo4j console

9. OPTIONAL: Add <NEO4J-Home>/bin/ to "PATH" if you're using bash

  • Open ~/.bashrc
  • add this line:
    PATH=$PATH:<NEO4J-HOME>/bin
  • Save and exit

10. Create Neo4j account

  • Open localhost:7474 in your web browser.
  • Login with the following credentials:
       Username: neo4j
       Password: neo4j
       Change the password to: pgdb.

Install Conda and Set up Conda Environment

For Intel CPUs (otherwise change the Anaconda version)

    curl https://repo.anaconda.com/archive/Anaconda3-2023.03-1-MacOSX-x86_64.sh -o ~/Downloads/Anaconda3-2023.03-1-MacOSX-x86_64.sh
    bash ~/Downloads/Anaconda3-2023.03-1-MacOSX-x86_64.sh
    rm -r ~/Downloads/Anaconda3-2023.03-1-MacOSX-x86_64.sh
    conda --version
    conda env create -f environment.yml

To start Conda environment

    conda activate pgdb

Install Maven

    brew install maven
	mvn --version

Setup dummy dataset

1. Download the test sample database to your Downloads folder.

2. Load the dump file into your own database.

    <NEO4J-HOME>/bin/neo4j-admin load --from=$HOME/Downloads/merged.dump --database=neo4j --force

TODO: Install Frontend requirements