Speed up creating escapevariants environment

[johnbradley]

Creating the escapevariants conda environment is taking a really long time. The README says to run conda env create -f environment.yml. This command takes over an hour on the Solving environment step:

$ conda env create -f environment.yml 
Collecting package metadata (repodata.json): done
Solving environment: \ 

[johnbradley]

One option is to use mamba to install the packages. Conda can install mamba so one option would be to run:

conda install mamba -n base -c conda-forge
mamba env create -f environment.yml 

This will install mamba into the conda base environment. Then use mamba to create the escapevariants environment.

Aside: Mamba is highly recommended by Snakemake.

[wodanaz]

looks like mamba is really fast to setup the environments. I tried in Azure and it worked. I failed to install it in Hardac, maybe because I don't have the privilege, I think.

[johnbradley]

On HARDAC you would not have permission to modify the base environment. You would need to put mamba in another environment then activate that then install. Creating an environment module with mamba might also be a possibility.

[johnbradley]

This was fixed by switching to Snakemake: #67 Snakemake uses mamba to handle installing requirements quickly.