conda install takes a VERY long time to solve

[danudwary]

I'm not certain why, but I've noticed that using conda to install emeraldbgc takes a very long time to solve. I just created a fresh env with conda create -n emerald -c bioconda emeraldbgc and it took almost 4.5 hours to solve. I am using the most recent miniconda on our HPC system, but I observed the same problem with a vanilla anaconda on a different machine, each of which are using the new mamba-based "fast" solver. My hardware is quite standard amd64 cpus, so there shouldn't be any strangeness with bioconda packages, and other conda installs work as expected. Additional data points: Adding new packages into the newly created emerald env takes no time at all to solve. And exporting an environment.yaml and re-importing works quickly, too.

Any ideas? Is this just me?

[SantiagoSanchezF]

I cannot think of anything obvious causing the issue.

We've been working on SanntiS, which is a fork of emeraldbgc, with some minor modifications and should be slightly faster. This repo is intended to be the main one.

I just created the env with conda create -n sanntis -c bioconda sanntis, and it took less that 10 minutes.

I hope this helps