Thanks Mark! Is Forester on maven to avoid external jar file dependency? On 10/17/12 9:18 PM, "Andreas Prlic" <[email protected]> wrote:
>Awesome, Mark, Thanks for fixing this! > >Andreas > >On Wed, Oct 17, 2012 at 6:08 PM, Mark Chapman <[email protected]> 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" <[email protected]> >>> To: "Scooter Willis" <[email protected]> >>> Cc: "Andreas Prlic" <[email protected]>, "Peter Bradbury" >>> <[email protected]>, "Jeff Glaubitz" <[email protected]>, "Ed Buckler" >>> <[email protected]>, "[email protected]" <[email protected]> >>> 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 <[email protected]> >>> 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" <[email protected]> >>>> To: "Terry Casstevens" <[email protected]> >>>> Cc: "Peter Bradbury" <[email protected]>, "Jeff Glaubitz" >>>> <[email protected]>, "Ed Buckler" <[email protected]>, >>>> "[email protected]" <[email protected]> >>>> 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 <[email protected]> >>>> 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 >>>> >>>> _______________________________________________ >>>> Biojava-l mailing list - [email protected] >>>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l >_______________________________________________ >Biojava-l mailing list - [email protected] >http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
