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Check out code from SVN
BioJava requires Subversion (SVN) and Maven for checking out the code and creating a build. Access is possible either via
- Anonymous SVN or GIT access or - Developer SVN access (ssh account required) or - BioJava SNAPSHOT builds (anonymous, Maven required)
Downloading and updating code via Anonymous SVN
The code.open-bio.org server offers up read-only copies of source code repositories via anonymous SVN. A list of code repositories available via SVN can be seen here: http://code.open-bio.org/?root=biojava
Checking out the latest BioJava code
The following example shows how to obtain the latest BioJava codebase snapshot using anonymous SVN, it will check out the latest copy of biojava-live/ from the "SVN trunk" and will locally store it in a directory named "biojava" on your system:
svn co http://code.open-bio.org/repos/biojava/biojava-live/trunk ./biojava
Anonymous checkouts are now hosted at read only mirror at github. As such you can of course also use git to get a copy of the code:
git clone https://github.com/biojava/biojava.git
finally there is also a SVN interface to github:
svn co http://svn.github.com/biojava/biojava.git ./biojava
A list of all available projects in SVN can be obtained with:
svn list http://code.open-bio.org/repos/biojava
Troubleshooting Anonymous SVN
If you encounter an error while using the SVN client or SVN Web interface, the likely cause is that our server is in the middle of replicating the repository from the primary source. While the mirror and replication process occurs, it is not unusual for SVN client functionality to break temporarily.
The final step of our codebase replication process is to explicitly re-verify the health and status of each repository, this process takes a few moments but while it occurs the repository is "locked" and unavailable for access.
* Anonymous SVN repositories are updated/mirrored hourly from the primary developer server * Anonymous SVN repositories are verified and repaired (if necessary) every 20 minutes
If a SVN client error occurs for longer than 20 minutes, please report this to: support@helpdesk.open-bio.org
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>
Downloading and updating code via Developer SVN
For getting write access to BioJava you need a developer account on dev.open-bio.org. Details for how developers can check out the read/write enabled SVN see at Developer_Code_Access
Links
See also the SVN developers page in the OBF wiki
Repository News
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
