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‎_wikis/BioJava:GetStarted.md‎

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### UNIX Bourne-type shells (the default with most Linux distributions and MacOS 10.3)
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`export CLASSPATH=/home/thomas/biojava.jar:/home/thomas/bytecode.jar:`
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`export CLASSPATH=/home/thomas/biojava-live.jar:/home/thomas/bytecode.jar:`
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`                        /home/thomas/commons-cli.jar:`
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`                        /home/thomas/commons-collections-2.1.jar:`
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`                        /home/thomas/commons-dbcp-1.1.jar:`
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`                        /home/thomas/commons-pool-1.1.jar:.`
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In some distributions of Biojava, you need to specify biojava.jar
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instead of biojava-live.jar in the above. We are working on resolving
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this.
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### UNIX C-type shell (for example: versions of Mac OS X pre-10.3)
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`setenv CLASSPATH /home/thomas/biojava.jar:/home/thomas/bytecode.jar:`
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`setenv CLASSPATH /home/thomas/biojava-live.jar:/home/thomas/bytecode.jar:`
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`                        /home/thomas/commons-cli.jar:`
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`                        /home/thomas/commons-collections-2.1.jar:`
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`                        /home/thomas/commons-dbcp-1.1.jar:`
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`                        /home/thomas/commons-pool-1.1.jar:.`
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In some distributions of Biojava, you need to specify biojava.jar
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instead of biojava-live.jar in the above. We are working on resolving
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this.
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### Windows from command line
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`set CLASSPATH C:\biojava.jar;C:\bytecode.jar;C:\commons-cli.jar;`
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`set CLASSPATH C:\biojava-live.jar;C:\bytecode.jar;C:\commons-cli.jar;`
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`                        C:\commons-collections-2.1.jar;C:\commons-dbcp-1.1.jar;`
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`                        C:\commons-dbcp-1.1.jar;.`
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In some distributions of Biojava, you need to specify biojava.jar
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instead of biojava-live.jar in the above. We are working on resolving
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this.
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### Windows autoexec.bat files
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`set CLASSPATH=C:\biojava.jar;C:\bytecode.jar;C:\commons-cli.jar;`
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`set CLASSPATH=C:\biojava-live.jar;C:\bytecode.jar;C:\commons-cli.jar;`
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`                        C:\commons-collections-2.1.jar;C:\commons-dbcp-1.1.jar;`
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`                        C:\commons-pool-1.1.jar;.`
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In some distributions of Biojava, you need to specify biojava.jar
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instead of biojava-live.jar in the above. We are working on resolving
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this.
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It is also possible to "install" JAR files onto your system by copying
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them into your Java installation's extensions directory. On most Unix
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systems, this is named *${JAVA\_HOME}/jre/lib/ext*. On Mac OS X there is

‎_wikis/BioJava:GetStarted.mediawiki‎

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=== UNIX Bourne-type shells (the default with most Linux distributions and MacOS 10.3) ===
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export CLASSPATH=/home/thomas/biojava.jar:/home/thomas/bytecode.jar:
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export CLASSPATH=/home/thomas/biojava-live.jar:/home/thomas/bytecode.jar:
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/home/thomas/commons-cli.jar:
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/home/thomas/commons-collections-2.1.jar:
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/home/thomas/commons-dbcp-1.1.jar:
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/home/thomas/commons-pool-1.1.jar:.
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In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. We are working on resolving this.
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=== UNIX C-type shell (for example: versions of Mac OS X pre-10.3)===
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setenv CLASSPATH /home/thomas/biojava.jar:/home/thomas/bytecode.jar:
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setenv CLASSPATH /home/thomas/biojava-live.jar:/home/thomas/bytecode.jar:
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/home/thomas/commons-cli.jar:
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/home/thomas/commons-collections-2.1.jar:
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/home/thomas/commons-dbcp-1.1.jar:
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/home/thomas/commons-pool-1.1.jar:.
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In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. We are working on resolving this.
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=== Windows from command line ===
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set CLASSPATH C:\biojava.jar;C:\bytecode.jar;C:\commons-cli.jar;
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set CLASSPATH C:\biojava-live.jar;C:\bytecode.jar;C:\commons-cli.jar;
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C:\commons-collections-2.1.jar;C:\commons-dbcp-1.1.jar;
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C:\commons-dbcp-1.1.jar;.
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In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. We are working on resolving this.
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=== Windows autoexec.bat files ===
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set CLASSPATH=C:\biojava.jar;C:\bytecode.jar;C:\commons-cli.jar;
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set CLASSPATH=C:\biojava-live.jar;C:\bytecode.jar;C:\commons-cli.jar;
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C:\commons-collections-2.1.jar;C:\commons-dbcp-1.1.jar;
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C:\commons-pool-1.1.jar;.
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In some distributions of Biojava, you need to specify biojava.jar instead of biojava-live.jar in the above. We are working on resolving this.
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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.
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You can now compile and run BioJava programs using the ''javac'' and ''java'' commands. You might like to look at the [[BioJava:Tutorial|tutorial]], [http://www.biojava.org/docs/api15b/index.html API documentation] and the [[BioJava:Cookbook |BioJava in anger]] section . Finally, you can learn a lot about BioJava by trying the demo programs included in the source distribution (see below).

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