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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)
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.
You can install BioNetDB from the binaries or from the source code. Next sections describe both methods in details.
Building using binaries
Download the latest release from GitHub.
Extract the contents of the archive using tar -xfz <filename> for the .tar.gz file, or gunzip <filename> for the .zip file.
- Run the BioNetDB command line: build/bin/bionetdb.sh
Building from source code
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. The following tools are required for successful build:
As mentioned, you get the BioNetDB source code from GitHub by downloading the tar ball or by cloning the git repository. Next sections describe both methods to get the source code.
Downloading the tar ball
Download the latest release from GitHub (tar.gz or zip file).
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
Execute one of the following git commands:
Code Block language bash theme RDark title Shell
## 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.git
Compiling BioNetDB source code
Once you get source the BioNetDB
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