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
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.
If you prefer to use SVN, code can also be accessed using Github's SVN bridge.
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>
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 BioJava:MavenMigration
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