[InterMine Dev] Generic GFF3 source

julie at flymine.org julie at flymine.org
Fri Mar 1 17:22:09 GMT 2013


So this path does exist:

/home/intermine/bio/sources/csfg-aniger-gff/main/resources

> Hi,
> I've created a custom GFF source for a previous version of my project, but
> I'd like to use the generic GFF3 source for InterMine v1.2, but I'm
> getting
> the following error message:
>
> integrate:
> [integrate] action:
>
> BUILD FAILED
> /home/intermine/imbuild/integrate.xml:54: Error in project.xml: Can't find
> directories for sources: 'gff3',  looked in:
>
> /home/intermine/bio/sources/example-sources/malaria-gff/main/src/org/intermine/bio
> [...]
>
> It seems that there's no GFF3 source. And the documentation is a bit
> inconsistent on that matter: it says at first that you need to create a
> specific data source, then it says it's optional.
>
> Same on the page to create the GFF data source: it says that just creating
> the data source will work as is, but I get the following error message
> (ran
> build after creating the source and updating project.xml):
>
> BUILD FAILED
> /home/intermine/imbuild/integrate.xml:54: The following error occurred
> while executing this line:
> /home/intermine/imbuild/library.xml:78: The following error occurred while
> executing this line:
> /home/intermine/imbuild/library.xml:141:
> /home/intermine/bio/sources/csfg-aniger-gff/main/resources does not exist.
>  at
> org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:483)
> at org.apache.tools.ant.taskdefs.Zip.grabResources(Zip.java:1547)
>  at org.apache.tools.ant.taskdefs.Zip.getResourcesToAdd(Zip.java:1286)
> at org.apache.tools.ant.taskdefs.Zip.getResourcesToAdd(Zip.java:1220)
>
> So is there a generic GFF source, or should I implement a custom one?
>
> Thanks!
> Thomas
>
> --
> Thomas Triplet, Jr. Eng., Ph.D.
> http://www.thomastriplet.net
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