[InterMine Dev] Generic GFF3 source

Thomas TRIPLET thomastriplet at gmail.com
Fri Mar 1 17:17:02 GMT 2013


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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