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DecodeGenetics / Ratatosk

Hybrid error correction of long reads using colored de Bruijn graphs
BSD 2-Clause "Simplified" License
94 stars 7 forks source link

version 0.9.0 on conda error #51

Closed juyanmei closed 6 months ago

juyanmei commented 6 months ago

The version 0.9.0 on conda seems to have an issue. After installing Ratatosk using this command 'conda install bioconda::ratatosk', I get an 'Illegal instruction' error when I try to run it. When I try using an older version on conda with 'conda install bioconda::ratatosk=0.7.6.3' or by cloning the Git repository and installing it, the program runs fine. If you could update the Ratatosk version on conda, that would be great. Thanks!

GuillaumeHolley commented 6 months ago

Hi @juyanmei,

The package was updated from Ratatosk 0.7.6.3 to 0.9.0 but I suspect there is a problem with the maximum k-mer size of its dependency Bifrost (which is a compile time parameter). That being said, I am not the author nor the maintainer of the bioconda package for Ratatosk. And I am not too fond of bioconda in general. I'll try to see what I can do but to be honest, this is low priority on my todo list. I would advise you to install Ratatosk from source as it is very easy (see https://github.com/DecodeGenetics/Ratatosk#installation), most likely as easy as installing it from bioconda imo.

Best, Guillaume

juyanmei commented 6 months ago

Thank you for your reply. Sorry, I thought you were the maintainer of the bioconda package for Ratatosk. I’ve successfully installed Ratatosk 0.9.0 from GitHub, and it was indeed quite easy.