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This is as a Lab Notebook which describes how to solve a specific problem at a specific time. Please keep this in mind as you read and use the content. Please pay close attention to the date, version information and other details.

Installing Bactopia on the HPCC (2022-10-03)

Bactopia is a bacteria genome analysis tool. It can be found at https://bactopia.github.io/v2.1.1/ and has extensive documentation. However, if you follow the instructions for installation on the MSU HPCC you may run into issues with solving the Python environment with Conda.

Installation steps:

module load Conda/3

Download miniconda https://docs.conda.io/en/latest/miniconda.html

Activate the miniconda environment

Install mamba

conda install -c conda-forge -c bioconda mamba

Update mamba:

conda install -c conda-forge 'mamba>=0.24.*'

Downloaded and activate bactopia:

mamba create -n bactopia -c conda-forge -c bioconda bactopia
conda activate bactopia

For further information, see this github issue: https://github.com/bactopia/bactopia/issues/355