[Biojava-l] maven question

[Daniel Quest]

Thanks for the tip Andreas,

It is still not working for me.  here is a 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/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>

  <groupId>gov.ornl</groupId>
  <artifactId>foo</artifactId>
  <version>1.0-SNAPSHOT</version>
  <packaging>jar</packaging>

  <name>foo</name>
  <url>http://maven.apache.org</url>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
  </properties>

  <dependencies>
       <dependency>
            <groupId>org.biojava</groupId>
            <artifactId>biojava3-core</artifactId>
            <version>3.0.1</version>
            <type>jar</type>
            <scope>compile</scope>
        </dependency>
  </dependencies>
  <repositories>
    <repository>
<id>biojava-maven-repo</id>
<name>BioJava repository</name>
<url>http://www.biojava.org/download/maven/</url>
 </repository>
</repositories>
</project>


and here is the code that does not recognize:
import org.biojava3.core.sequence.ProteinSequence;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava3.core.sequence.io.FastaReader;
import org.biojava3.core.sequence.io.FastaReaderHelper;
import org.biojava3.core.sequence.io.GenericFastaHeaderParser;
import org.biojava3.core.sequence.io.ProteinSequenceCreator;

nothing fancy yet.  Any other ideas?

Thanks
-Daniel

On Thu, Jul 21, 2011 at 1:55 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Daniel,
>
> you correctly specify where to get the .jars from, but you also need
> to specify which of the modules you want to depend on. e.g.:
>
>        <dependency>
>                        <groupId>org.biojava</groupId>
>                         <artifactId>biojava3-core</artifactId>
>                         <version>3.0.1</version>
>                         <type>jar</type>
>                        <scope>compile</scope>
>                </dependency>
>
> Andreas
>
>
>
> On Thu, Jul 21, 2011 at 10:47 AM, Daniel Quest <daniel.quest at gmail.com>
> wrote:
> > Hey all,
> >
> > not sure what the maven dependancy should be to get biojava to work in a
> > maven project.
> >
> > I tried:
> >
> >  <dependencies>
> >        <dependency>
> >            <groupId>org.biojava</groupId>
> >            <artifactId>biojava</artifactId>
> >        <version>3.0.1</version>
> >        </dependency>
> >  </dependencies>
> >
> > But that does not appear to be working in intellij
> >
> > I did do:
> >  <repositories>
> >    <repository>
> > <id>biojava-maven-repo</id>
> > <name>BioJava repository</name>
> > <url>http://www.biojava.org/download/maven/</url>
> >  </repository>
> > </repositories>
> >
> > does someone have an example pom.xml file for projects that use BioJava?
> > Thanks
> > -Daniel
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>