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

[Peng Yu]

Hi,

I installed eclipse-java-kepler-R-macosx-cocoa-x86_64.tar.gz.

I'm now following this step. But I don't set 'm2e - Maven Integration
for Eclipse'. Is the tutorial for previous versions of eclipse but not
the current version?

http://biojava.org/wiki/BioJava3_eclipse#Plugin_Installation

On Tue, Jul 23, 2013 at 8:16 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
> 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
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>
>
>
> -



-- 
Regards,
Peng