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Yandell-Lab / maker

Genome Annotation Pipeline
http://yandell-lab.org/software/maker.html
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maker 3.01.04 “ERROR: Could not determine if RepBase is installed” #1

Open N0s3n opened 2 years ago

N0s3n commented 2 years ago

In RepeatMasker/4.1.2-p1, they've changed their database filetypes from .embl to .h5. And masker is checking for .embl files before it runs.

Add a check for .h5 files on line 4972 in lib/GI.pm. 

4971        $lib .= "Libraries/RepeatMaskerLib.embl";
4972        die "ERROR: Could not determine if RepBase is installed\n" if(! -f $lib);

And please modify the two exact error messages when checking for RepeatMasker on line 4969 and 4972.

andrewSharo commented 2 years ago

I ran into this error today and manually fixed it on my own copy of maker, so this is just a reminder to address this in future releases of maker. Is there a reason maker does not support dfam?

euduca commented 1 year ago

Hi @andrewSharo .

Can you show us how to fix it?

Thanks.

andrewSharo commented 1 year ago

Hi @euduca as far as I can recall, I just followed N0s3n's instructions above