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

[Andreas Prlic]

Yes, those instructions were made for  Juno. I have not upgraded to Kepler
as of yet and can't comment if this still works exactly the same...

Andreas


On Tue, Jul 23, 2013 at 6:46 AM, Peng Yu <pengyu.ut at gmail.com> wrote:

> 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
>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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