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Getting Started

The first thing we'll need to do is get Bactopia installed, and for this we'll use Conda.

Goals for this Section

  • (Optional) Install MambaForge
  • Create a Bactopia Environment
  • Verify v3.0.0 of Bactopia is installed

(Optional) Install MambaForge

If you do not have Conda installed I recommend installing MambaForge, as it comes with Mamba pre-installed. You'll want to follow the MambaForge Install Instructions for this. This will take a few minutes, but once complete you'll be ready to install Bactopia.

Installation

At the time of writing this, Bactopia is undergoing a major version change (v2 -> v3). Because of this inbound change, I felt it best to avoid using v2 for this workshop. So, we'll be installing a development build of Bactopia. This build includes a preview to version 3 of Bactopia.

mamba create -n bactopia-dev -c rpetit3 -c conda-forge -c bioconda bactopia

If all goes well you should now have Bactopia v3 installed.

Verify Version Installed

Let's go ahead and activate the new environment, and we'll make sure the correct version is installed. For this we'll use --version:

conda activate bactopia-dev
bactopia --version
bactopia 3.0.0

If successful, you are ready to proceed to Bactopia Subcommands!