[Biojava-l] maven question

[Andreas Prlic]

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 <daniel.quest at gmail.com> 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 <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
>> -----------------------------------------------------------------------
>
>