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DecodeGenetics / Ratatosk

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

Installation typo & Docker #30

Closed hoelzer closed 3 years ago

hoelzer commented 3 years ago

Hi all,

thanks for the tool! We are currently testing it in the context of a fungi hybrid assembly pipeline w/ various tools/polishers.

One thing I noticed:

git clone --recursive https://github.com/DecodeGenetics/Ratatosk/Ratatosk.git

in the README should be

git clone --recursive https://github.com/DecodeGenetics/Ratatosk.git

and we also build a Docker container to easily integrate the tool into a (nextflow) pipeline. If you want to use the Container as well, it's here:

docker pull nanozoo/ratatosk:0.1--73685af

(I still need to test the container properly, but should work)

GuillaumeHolley commented 3 years ago

Hi @hoelzer,

Thank you for the typo (fixed) and the container, that's fantastic work! I'll try to test the container asap but I am mostly working on an air-gapped cluster so containers are a little bit tricky to use for me. We'll see how it goes. Let me know how Ratatosk works for your assembly/polishing pipeline. As a short note, I am probably gonna push this week a new version that works better than the current one :)

Guillaume

hoelzer commented 3 years ago

Hi @GuillaumeHolley ah that's great to hear! I can then easily set up a new container with that version :)

We also just tested the container in our pipeline: seems to work all fine!

Cheers, Martin