pangolin update

[wodanaz]

Pangolin creators recommend to update pangolin every time before using in order to update the most recent set of variants as new variants may appear in populations.

I couldn't find the 'conda activate pangolin' line in the scripts anymore. Where would be the best place to update pangolin?

Thanks

[johnbradley]

Previously you had to manually activate the pangolin conda before running the scripts. We are now using the escapevariants conda environment which contains all software used by the pipeline. You could update pangolin there. Something like:

module load Anaconda3
conda activate escapevariants
pangolin --update

---

To better document the intent of running the latest version perhaps we should remove the version from the conda environment: https://github.com/wodanaz/Assembling_viruses/blob/916731fddb4bc7026aeaab327e7703b0d703a3ea/environment.yml#L7

[wodanaz]

gotcha!

thanks!