Hi Daniel, your pom works fine in my eclipse setup (did a basic maven project and copy and pasted your pom XML).
- Where is your .java file located? It should be somewhere under .../src/main/java - Did you try a "mvn clean package install" ? Andreas On Thu, Jul 21, 2011 at 11:13 AM, Daniel Quest <[email protected]> wrote: > 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 <[email protected]> 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 <[email protected]> >> 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 - [email protected] >> > 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 >> ----------------------------------------------------------------------- > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
