[Biojava-l] Biojava Dependency on Forester

Scooter Willis HWillis at scripps.edu
Thu Oct 18 01:49:24 UTC 2012 

Thanks Mark! Is Forester on maven to avoid external jar file dependency?

On 10/17/12 9:18 PM, "Andreas Prlic" <andreas at sdsc.edu> wrote:

>Awesome, Mark, Thanks for fixing this!
>
>Andreas
>
>On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <chapman at cs.wisc.edu> wrote:
>> biojava3-alignment and biojava3-phylo have both been updated to use the
>> latest forester release: 1.005.  The jar file is in our maven
>>repository,
>> and changes are committed to the SVN and git repositories.
>>
>> Enjoy!
>> Mark
>>
>>
>>
>> On 10/11/2012 02:50 PM, Scooter Willis wrote:
>>>
>>> Andreas
>>>
>>> Looks like the alignment code is using the distance matrix from
>>>forester
>>> and that has changed. Any chance the developer who did the MSA code
>>>could
>>> get this working with the latest forester code. It is probably a
>>>refactoring
>>> problem.
>>>
>>> Scooter
>>>
>>> ----- Reply message -----
>>> From: "Terry Casstevens" <tmc46 at cornell.edu>
>>> To: "Scooter Willis" <HWillis at scripps.edu>
>>> Cc: "Andreas Prlic" <andreas.prlic at gmail.com>, "Peter Bradbury"
>>> <pjb39 at cornell.edu>, "Jeff Glaubitz" <jcg233 at cornell.edu>, "Ed Buckler"
>>> <esb33 at cornell.edu>, "biojava-l at biojava.org" <biojava-l at biojava.org>
>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>> Date: Thu, Oct 11, 2012 2:56 pm
>>>
>>>
>>>
>>> Hi Scooter, Andreas,
>>>
>>> Thank you again for the responses.
>>>
>>> This is one problem we are seeing.  org/forester/phylogenyinference
>>> does not exist in Forester version 1.005.
>>>
>>> Exception in thread "main" java.lang.NoClassDefFoundError:
>>> org/forester/phylogenyinference/DistanceMatrix
>>> at
>>> 
>>>org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignment
>>>s.java:176)
>>> at
>>> 
>>>net.maizegenetics.gbs.maps.TagsAtLocus.getVariableSites(TagsAtLocus.java
>>>:306)
>>> at
>>> 
>>>net.maizegenetics.gbs.maps.TagsAtLocus.getSNPCallsQuant(TagsAtLocus.java
>>>:183)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.addSitesToMuta
>>>bleAlignment(TagsToSNPByAlignmentPlugin.java:417)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.runTagsToSNPBy
>>>Alignment(TagsToSNPByAlignmentPlugin.java:347)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TagsToSNPByAlignmentPlugin.performFunctio
>>>n(TagsToSNPByAlignmentPlugin.java:107)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TerryPipelines.runTagsToSNPByAlignmentPlu
>>>gin(TerryPipelines.java:36)
>>> at
>>> 
>>>net.maizegenetics.gbs.pipeline.TerryPipelines.main(TerryPipelines.java:4
>>>1)
>>> Caused by: java.lang.ClassNotFoundException:
>>> org.forester.phylogenyinference.DistanceMatrix
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
>>> at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:423)
>>> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
>>> at java.lang.ClassLoader.loadClass(ClassLoader.java:356)
>>>
>>>
>>> Thank you,
>>>
>>> Terry
>>>
>>>
>>> On Thu, Oct 11, 2012 at 2:46 PM, Scooter Willis <HWillis at scripps.edu>
>>> wrote:
>>>>
>>>> If forester has maven repository we can unhook the local depedency. We
>>>> use
>>>> forester for NJ and should only be a needed in one model. Let me know
>>>>the
>>>> issue/conflict and I can see what I can do to clean up.
>>>>
>>>> Thanks
>>>>
>>>> Scooter
>>>>
>>>>
>>>> ----- Reply message -----
>>>> From: "Andreas Prlic" <andreas.prlic at gmail.com>
>>>> To: "Terry Casstevens" <tmc46 at cornell.edu>
>>>> Cc: "Peter Bradbury" <pjb39 at cornell.edu>, "Jeff Glaubitz"
>>>> <jcg233 at cornell.edu>, "Ed Buckler" <esb33 at cornell.edu>,
>>>> "biojava-l at biojava.org" <biojava-l at biojava.org>
>>>> Subject: [Biojava-l] Biojava Dependency on Forester
>>>> Date: Thu, Oct 11, 2012 2:33 pm
>>>>
>>>>
>>>>
>>>> Hi Terry,
>>>>
>>>> Biojava depends on forester version 0.955. There are no plans to get
>>>> rid of this dependency, as far as I know. However we can try to
>>>> upgrade to a newer version if that helps.
>>>>
>>>> If you are working in a Maven environment and you pull in BioJava that
>>>> way, you can add an exclusion to your config. Something like the XML
>>>> below. This forces your project to ignore the older forester library
>>>> configured in biojava. Is this a suitable workaround for your problem?
>>>>
>>>> Andreas
>>>>
>>>>
>>>>          <dependency>
>>>>                          <groupId>org.biojava</groupId>
>>>>                          <artifactId>biojava3-phylo</artifactId>
>>>>                          <version>3.0.4</version>
>>>>                          <exclusions>
>>>>                                  <exclusion>
>>>>                                          <groupId>org</groupId>
>>>>
>>>> <artifactId>forester</artifactId>
>>>>                                  </exclusion>
>>>>                          </exclusions>
>>>>                  </dependency>
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Oct 11, 2012 at 11:17 AM, Terry Casstevens <tmc46 at cornell.edu>
>>>> wrote:
>>>>>
>>>>> Dear Andreas,
>>>>>
>>>>> I am the lead developer of the software Tassel.
>>>>> http://www.maizegenetics.net/tassel
>>>>>
>>>>> We currently use Biojava 3.0.  And we are
>>>>> wanting to use the latest release of Forester.
>>>>> Since Biojava has a dependency on an older
>>>>> release of Forester, we are running into conflicts.
>>>>> Can you help explain Biojava's dependency on
>>>>> Forester?
>>>>>
>>>>> What version of Forester does Biojava 3.0 require?
>>>>> It looks like version 0.955
>>>>>
>>>>> What version of Forester does Biojava 3.0.4 require?
>>>>>
>>>>> Does any Biojava jar files include Forester classes?
>>>>> Or just references?
>>>>>
>>>>> Are there plans to remove Biojava's dependency
>>>>> on Forester?
>>>>>
>>>>>
>>>>> Thank you,
>>>>>
>>>>> Terry Casstevens
>>>>
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>>>
>>>
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