Quick Start

Installation via Conda

This is as quick as it gets. The following commands will install Bactopia and run a test dataset.

# Install Bactopia using Conda
conda create -y -n bactopia -c conda-forge -c bioconda bactopia

# Test Bactopia
# First launch will set up environments (e.g. Conda, Docker, or Singularity)
conda activate bactopia
bactopia -profile test,standard

The first run might take a while

The first time you run Bactopia it will build the environments (Conda, Docker, or Singularity) needed for analysis. Depending on your internet connection this might take a little while. I recommend grabbing a coffee or going for a walk. This is only a one time build, future runs will be much faster.

note

Use -profile to change environment

The default profile for Bactopia is Conda. If you would like to test using Docker or Singularity, you can use the -profile option. For example, to use Docker you would use -profile test,docker, and -profile test,singularity for Singularity.

Run from GitHub Repository

Alternatively, if you already have Nextflow installed, and you don't want to use Conda to install Bactopia, you can run Bactopia directly from the GitHub repository.

nextflow run bactopia/bactopia -profile test,standard

Missing out on helper commands

The Conda install of Bactopia comes with a few helper commands that are not available when running directly with Nextflow. These include commands to help prepare sample sheets, search public databases, pre-build environments, among other helper tools.