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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)
- Apache Tomcat Web server
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.
In order to install Tomcat Web server, follow the instruction from the Apache Software Foundation.
BioNetDB installation requires the configuration file configuration.yml written in YAML format and located in the $BIONETDB_HOME folder. The configuration file contains mainly Neo4j database configuration, e.g.:
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. You can download the tar ball or clone 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:
Compiling BioNetDB source code
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:
- java-common-libs:https://github.com/opencb/java-common-libs (branch 'develop')
- biodata: https://github.com/opencb/biodata (branch 'develop')
- cellbase: https://github.com/opencb/cellbase (branch 'develop')
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:
Now you can compile the BioNetDB source code by executing the following command from your BioNetDB folder (i.e., the root of the cloned repository):
After compiling successfully, you should see the following messages:
Deploy WAR file
Once BioNetDB compiled, the WAR file (bionetdb.war) is located at the $BIONETDB_HOME folder. The WAR file consists of a set of RESTful webservices acting as an interface to BioNetDB. In order to start the web services follow the next steps:
Install and start the Apache Tomcat Web server. Be sure you set the environment variable $BIONETDB_HOME pointing to your BioNetDB folder before starting Tomcat server.
Deploy bionetdb.war by just copying it from the BioNetDB folder (i.e., $BIONETDB_HOME) into the Tomcat
webappsfolder (check the folder where you downloaded Tomcat, or probably
/var/lib/tomcat8if you installed via apt-get):
- Then, you should be able to see the swagger page at
http://localhost:8080/bionetdb/webservices/. See Using RESTful web services for a tutorial.
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