Get source

BioJava is hosted on Github. The preferred method for checking out the source is with git, although it is also possible to use subversion. This page contains general instructions for getting the BioJava source. Users of the Eclipse IDE can see more detailed instructions at BioJava3 eclipse.

Getting the latest release code

BioJava can be accessed several ways

Git
SVN (not recommended)
Download binaries
Directly from Maven

Using git

The latest stable release version of BioJava is available through git using the following command:

git clone https://github.com/biojava/biojava.git

This can also be done directly from within Eclipse. Instructions are available at BioJava3 eclipse.

Using SVN

If you prefer to use SVN, code can also be accessed using Github’s SVN bridge.1

svn co http://svn.github.com/biojava/biojava.git ./biojava

Maven Release builds

In order to use BioJava in your Maven projects, add the following lines to your project .pom file:

<repositories>
    <repository>
        <id>biojava-maven-repo</id>
        <name>BioJava repository</name>
        <url>http://www.biojava.org/download/maven/</url>
        <releases>
            <enabled>true</enabled>
        </releases>
    </repository>
</repositories>

You can then add any of the biojava modules as a dependency for your project and Maven will automatically fetch the relevant jar files.

Getting the latest development code

BioJava generally releases two to three times a year. To get the latest features and bug fixes, you can use the devel branch.

git clone -b devel https://github.com/biojava/biojava.git

or from an existing git repository

git checkout devel

All developers should use the devel branch for publishing changes. Details for how to contribute changes back to BioJava are available at Developer_Code_Access.

Maven SNAPSHOT builds

BioJava now also provides SNAPSHOT builds of the latest code base. This is created automatically by the automated build system at [http://emmy.rcsb.org:8080/cruisecontrol/ ]. In order to install .jar files from this repository automatically for your Maven projects, add the following lines to your project .pom file:

<repositories>
    <repository>
        <id>biojava-maven-repo</id>
        <name>BioJava repository</name>
        <url>http://www.biojava.org/download/maven/</url>
        <snapshots>
            <enabled>true</enabled>
        </snapshots>
        <releases>
            <enabled>true</enabled>
        </releases>
    </repository>
</repositories>

History

At its conception, BioJava was stored on a CVS repository and built using Ant. Since then, several major refactoring have occurred leading to the current layout as a set of Maven modules stored on github.

BioJava migrated to Git

BioJava was migrated to git in April 2013 (see SVN to GIT Migration). History prior to September 2009 was not migrated. The old SVN repositories are still available for anonymous SVN access, but are closed to new commits. The repository can be browsed online or checked out using

svn co http://code.open-bio.org/repos/biojava/biojava-live/trunk ./biojava

Developers who previously had write access to SVN can also view the archive at the old development server (requires ssh access)

svn co svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/biojava-live/trunk/ ./biojava-live

BioJava migrated to Maven

BioJava has migrated to Maven and was re-organized into sub-modules. For more information see

As of September 2009 the new mavenized code is available through the main biojava trunk. The old ant-based biojava is still available in the branch trunk_1_7_ant

BioJava now using SVN

As of January 2008 BioJava has moved the version control system from CVS to Subversion (svn). All Biojava modules, branches and tags and the history of the files has been imported into the new repository. For more detailed documentation about the procedure used for the CVS to SVN migration see SVNmigrationHistory