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Missing chromosome_prefix and supercontig_prefix #153

Closed svengato closed 2 months ago

svengato commented 5 months ago

Each genome in the data store must specify these in their README.yml, otherwise the validator will detect it and make the InterMine build fail.

Can there be more than one supercontigprefix? For the Vicia genomes, it looks like `contigandptg` are both valid. (To do: rebuild the mine with one or both of these - I had tentatively set it to something else, so no supercontigs get added to the database.)

svengato commented 2 months ago

Using contig locally on lupini-mines.

To do: Remember to change the README and CHANGES files in the data store.

adf-ncgr commented 2 months ago

I think the current logic allows you to specify the chromosome_prefix without specifying a supercontig_prefix and anything that does not match the former will be considered a supercontig (allowing some heterogeneity). I'm not in love with this way of doing things, but it's probably workable for most situations.

svengato commented 2 months ago

It did expect a supercontig_prefix.

adf-ncgr commented 2 months ago

OK, looks like you can supply a comma-delimited list so I guess just do it that way

svengato commented 2 months ago

To do: Remember to change the README and CHANGES files in the data store.

Done.