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
