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[Ontology-editors] adding obo2obo to check pipeline

Chris Mungall cjm at berkeleybop.org
Fri Mar 19 14:56:06 PDT 2010


Mike et al

I've added a call to obo2obo to check-obo-for-standard-release.pl.

Although obo2obo is not guaranteed to fail for an invalid file because  
obo format is so loose, this should still allow us to proactively be  
buffered against a wider spectrum of possible things that could go  
wrong.

Note this is disabled by default. To enable it, run

	check-obo-for-standard-release.pl --enable-obo2obo-check  
gene_ontology_write.obo

Or change the script to remove this line

	$disabled{'obo2obo-check'} = 1;

Before you do this, you need to check that obo2obo is in the path  
available to the cron job. I believe this must already be the case as  
it's used in other portions of the pipeline, but I don't want to  
enable this by default until you've checked it.

Thanks.



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