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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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Error: The RMblast engine is not installed in RepeatMasker! #474

Closed tallnuttrbgv closed 4 months ago

tallnuttrbgv commented 4 months ago

I have manually installed EDTA and all it's dependencies (and their dependencies) they all appear to work normally. However:

EDTA.pl --repeatmasker /g/data/nm31/bin/RepeatMasker --check_dependencies

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Extensive de-novo TE Annotator (EDTA) v2.1.1
Shujun Ou (shujun.ou.1@gmail.com)

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Tue Jul 2 12:27:54 AEST 2024 Dependency checking: Error: The RMblast engine is not installed in RepeatMasker!

rmblast location is specified in the RepeatMaskerConfig.pm:

'value' => '/g/data/nm31/bin/rmblast-2.14.0/bin'

Also tried without /bin at end.

rmblast runs fine on it's own.

RepeatMasker also runs on it's own.

I do not have any other modules or RepeatMasker installs.

So what is the solution? It seems to be a very common problem when installing EDTA?

Thanks.

tallnuttrbgv commented 4 months ago

I notice in another comment dev has said only the mamba yml install method works - have now done this on a VM.