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Server Configuration

Requirements

In order to install BioNetDB, the following packages are required:

  • Java 1.8.0_60+
  • Neo4j graph database
  • Apache Maven (when building BioNetDB from sources)

Installing Neo4j

In order to install Neo4j, follow the instructions from the Neo4j Operation Manual powered by the Neo4j Team. This describes how to install Neo4j in different deployment contexts, such as Linux, Mac OS, Windows, Debian, Docker.

Installing BioNetDB

In order to build BioNetDB from source code you must first get the source code of BioNetDB from GitHub, most of the dependencies - including OpenCB dependencies - will be fetched from Maven Central Repository, however in some scenarios OpenCB dependencies will need to be built from GitHub source code. Compiling and building processes are carried out by Apache Maven.

As mentioned, you get the BioNetDB source code from GitHub by downloading . You can download the tar ball or by cloning clone the git repository. Next sections describe both methods to get the source code. 

Downloading the tar ball

  1. Download the latest release from GitHub (tar.gz or zip file).

  2. Extract the contents of the archive using tar -xfz <filename> for the tar.gz file, or gunzip <filename> for the zip file.

Cloning the BioNetDB git repository

  1. Execute one of the following git commands:

    Code Block
    languagebash
    themeRDark
    titleShell
    ## Latest stable version
    git clone -b master https://github.com/opencb/bionetdb.git
    
    ## Develop branch, for this to work remember to clone and build BioNetDB dependencies (see below)
    git clone -b develop https://github.com/opencb/bionetdb.gitg


Compiling BioNetDB source code

Once you get source the BioNetDB 

BioNetDB has dependencies from other OpenCB projects such as CellBase while others are third-party dependencies such as MongoDB. All BioNetDB stable releases are always merged and tagged at master branch (users are encouraged to use latest stable release for production), you can find all releases at BioNetDB Releases. We guarantee that all the dependencies needed for building stable releases are deployed at Maven Central Repository, this is true for both OpenCB and third-party dependencies. Therefore for building a stable release you only need to clone BioNetDB repository itself since all the dependencies will be fetched form Maven Central repository.

This is different for development branches. Active BioNetDB development is carried out at develop branch, in this branch third-party dependencies will be still fetched from Maven Central Repository but this is not true for OpenCB dependencies since it is very likely they are still in development and therefore they are not deployed. Keep in mind that we only guarantee that  develop compiles and that bugs are expected, use this branch for development or for testing new functionalities. So, for building develop branch you may require to download and install the following OpenCB repositories in this order:

As you can see one of our rules is that develop branch of all major applications such as BioNetDB and CellBase always depend on develop branches. So, if you really want to build develop the you can clone and build dependencies by executing:

Code Block
languagebash
themeRDark
titleClone Dependencies
## Clone develop branc
git clone -b develop https://github.com/opencb/java-common-libs.git
git clone -b develop https://github.com/opencb/biodata.git
git clone -b develop https://github.com/opencb/cellbase.git

## Now you can execute the following command in each of the folders the specified order above
mvn clean install -DskipTests


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