BioJava:GetStarted

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If you want to modify BioJava, you can obtain a copy of the source code from the download areas. Source releases are distributed in .tar.gz format. You can also obtain up-to-the-minute source code via either the [http://biojava.org/download/maven/ Maven repository] or an [[CVS_to_SVN_Migration| anonymous SVN checkout]].
 
If you want to modify BioJava, you can obtain a copy of the source code from the download areas. Source releases are distributed in .tar.gz format. You can also obtain up-to-the-minute source code via either the [http://biojava.org/download/maven/ Maven repository] or an [[CVS_to_SVN_Migration| anonymous SVN checkout]].
  
BioJava is now built using [http://maven.apache.org/ Apache Maven].  
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BioJava is now built using [http://maven.apache.org/ Apache Maven].
 
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== Building the demo programs ==
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The source distribution contains a number of small demo programs. Once you have a working ''biojava.jar'' on your classpath, these can be compiled directly using ''javac'' from the demos directory.
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  (unix)
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  cd demos
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  javac seq/TestEmbl.java
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  java seq.TestEmbl seq/AL121903.embl
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  (windows)
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  cd demos
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  javac seq\TestEmbl.java
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  java seq.TestEmbl seq\AL121903.embl
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Revision as of 18:30, 11 January 2012

Contents

Introduction

BioJava will run on any computer with a Java virtual machine complying to the Java 2 Standard Edition (J2SE) 1.6 (or later) specifications. Java implementations for Linux, Windows, and Solaris are available to download from Oracle's java website. Recent versions of MacOS X include a suitable Java implementation as standard. Java is also available on many other platforms: if in doubt, contact your vendor. BioJava binaries are distributed in .jar (Java ARchive) format.

You can get the latest version BioJava3 (v3.0.1) (requires Java 1.6+) from the download area.

You can get the latest version BioJava1 (v1.8.1) (requires Java 1.5+) from the BJ1 download area .

You can also integrate BioJava with NetBeans IDE. To find out how follow this link.

A step by step guide on 'How to integrate BioJava in Nebtbeans IDE' is here.

Maven

BioJava usesMaven as a build and distribution system. If you are new to Maven, take a look at the Getting Started with Maven guide.

We are providing a BioJava specific Maven repository at http://biojava.org/download/maven/ .

You can add the BioJava repository by adding the following XML to your project pom.xml file:

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

        <dependencies>
                ...
                <dependency>
                        <groupId>org.biojava</groupId>
                        <artifactId>biojava3-core</artifactId>
                        <version>3.0.2</version>
                </dependency>
                <!-- other biojava jars as needed -->
        </dependencies>
	

Installation

None of these .jar files need to be unpacked for normal use -- simply place them in a convenient directory.

To use BioJava, add the required JAR files to your CLASSPATH environment variable. The exact syntax varies between platforms.

It is also possible to "install" JAR files onto your system by copying them into your Java installation's extensions directory. On most Unix systems, this is named ${JAVA_HOME}/jre/lib/ext. On Mac OS X there is a per-user extensions directory called ~/Library/Java/Extensions (you may have to create this directory yourself). For other platforms, consult your Java vendor.

You can now compile and run BioJava programs using the javac and java commands. You might like to look at the developer section on the Main page for documentation, cookbook and tutorials. Finally, you can learn a lot about BioJava by trying the demo programs included in the source distribution (see below).

Building your own

If you want to modify BioJava, you can obtain a copy of the source code from the download areas. Source releases are distributed in .tar.gz format. You can also obtain up-to-the-minute source code via either the Maven repository or an anonymous SVN checkout.

BioJava is now built using Apache Maven.

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