[Biojava-l] How to compile and run the demo in biojava3?

[Andreas Prlic]

you might want to learn how to use an IDE, such as eclipse.

http://biojava.org/wiki/BioJava3_eclipse

Andreas


On Mon, Jul 22, 2013 at 9:25 PM, Peng Yu <pengyu.ut at gmail.com> wrote:

> Hi,
>
> I see some demos in biojava3 source repository.
>
> ~/dvcs_src/biojava/biojava3-alignment/src/main/java/demo$ dir
> CookbookMSA.java  DemoAlignProteins.java  DemoLoadSubstMax.java
> TestDNANeedlemanWunsch.java
>
> I just learned how to use mvn to start a new project and added biojava
> info to pom.xml as in the following. But I'm not sure how to compile
> the demo and run it. Could anybody show the detailed procedure on how
> to use them? Thanks.
>
> ~/linux/test/java/maven/bin/mvn/my-app$ cat pom.xml
> <project xmlns="http://maven.apache.org/POM/4.0.0"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
>   xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
> http://maven.apache.org/maven-v4_0_0.xsd">
>   <modelVersion>4.0.0</modelVersion>
>   <groupId>com.mycompany.app</groupId>
>   <artifactId>my-app</artifactId>
>   <packaging>jar</packaging>
>   <version>1.0-SNAPSHOT</version>
>   <name>my-app</name>
>   <url>http://maven.apache.org</url>
>   <dependencies>
>     <dependency>
>       <groupId>junit</groupId>
>       <artifactId>junit</artifactId>
>       <version>3.8.1</version>
>       <scope>test</scope>
>     </dependency>
>     <dependency>
>       <groupId>org.biojava</groupId>
>       <artifactId>biojava3-core</artifactId>
>       <version>3.0.6</version>
>     </dependency>
>   </dependencies>
>   <repositories>
>     <repository>
>       <id>biojava-maven-repo</id>
>       <name>BioJava repository</name>
>       <url>http://www.biojava.org/download/maven/</url>
>     </repository>
>   </repositories>
> </project>
>
> --
> Regards,
> Peng
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