changed artic container

replikation commented 3 years ago

@iferres

added another container
i currently don't have compressed fast5 data available to test this.
could you confirm that it works?

nextflow pull replikation/poreCov && nextflow run replikation/poreCov -b fix137 --nanopolish (...)

conda installation took 2 or 3 days until the env was "resolved" ...

iferres commented 3 years ago

2 or 3 days 🤯 ! May be conda caught covid ¯_(ツ)_/¯... Have you tried mamba? Anyway, it's a lot of time. I built it on top of the Connor-Lab artic container and it didn't took that long. I see in the Dockerfile that they install mamba on top of continuumio/miniconda3 base image and then resolve the environment with it, although they could use the official mamba base image (https://hub.docker.com/r/mambaorg/micromamba).

Nice, thanks again @replikation . I'll ask my colleague to try it and come back to tell you.

replikation commented 3 years ago

thanks and yes good idea with mamba. still, it's getting annoying.. to handle python install conda, to handle conda install mamba ....

iferres commented 3 years ago

Hey @replikation , it worked! Thanks again

replikation / poreCov

changed artic container #139