Some questions about installing the Intermine

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Some questions about installing the Intermine

clemsonyfu
Hi, I'm a newbie, I met several problems when I tried to install the intermine in a CentOS PC box.

I installed the malariamine example successfully. I need to 1) add my own data, 2) integrate the gbrowse/jbrowse with the intermine.

1. I first deleted all of the files in the directory intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/gff and intermine_0_97/malariamine/integrate/DATA_DIR/malaria/genome/fasta, I copied my own files to the two directories.
when I tried to run (cd ~/intermine_0_97/malariamine/integrate; ant -Dsource=malaria-gff -v), I got:

java.lang.IllegalArgumentException: no class found in model for: Source (original GFF record type: source) for record: <GFF3Record: sequenceID: NC_012985.2 source: RefSeq type: source start: 1 end: 1226704 score: null strand: + phase: null attributes: {organism=[Candidatus Liberibacter asiaticus str. psy62], mol_type=[genomic DNA], strain=[psy62], db_xref=[taxon:537021]}>
at org.intermine.bio.dataconversion.GFF3Converter.process(GFF3Converter.java:173)
at org.intermine.bio.dataconversion.GFF3Converter.parse(GFF3Converter.java:126)
at org.intermine.bio.task.GFF3ConverterTask.execute(GFF3ConverterTask.java:241)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:416)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
at org.intermine.task.Integrate.performAction(Integrate.java:135)
at org.intermine.task.Integrate.execute(Integrate.java:127)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
at org.apache.tools.ant.Main.runBuild(Main.java:758)
at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

2. How to setup the gbrowse?
First, I copied the whole directory from ~/intermine_0_97/flymine/gbrowse/ to ~/intermine_0_97/malariamine/.

Then I followed the instructions in the document http://intermine.org/wiki/GBrowseConfiguration. I don't know where is the file build.properties.<mine>. I put it to ~/intermine_0_97/malariamine/gbrowse/build.properties.malariamine, and run ant write-gff. I get only error:

write-gff:

BUILD FAILED
java.lang.RuntimeException: no chromosomes found
at org.intermine.bio.gbrowse.WriteGFFTask.writeGFF(WriteGFFTask.java:271)
at org.intermine.bio.gbrowse.WriteGFFTask.execute(WriteGFFTask.java:110)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:616)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:357)
at org.apache.tools.ant.Target.performTasks(Target.java:385)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)
at org.apache.tools.ant.Project.executeTarget(Project.java:1306)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1189)
at org.apache.tools.ant.Main.runBuild(Main.java:758)
at org.apache.tools.ant.Main.startAnt(Main.java:217)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)

Anybody can help me to install the intermine? Thanks!!!

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