Installation requirements - StephenFordham/BacGenomePipeline GitHub Wiki

Installation requirements

Conda Install

The simplest way to install BacGenomePipeline is running the following command:

conda install -c stephenfordham bacgenomepipeline

I recommend installing BacGenomePipeline in a conda virtual environment: For example:

conda create -n pipeline

conda activate pipeline

(pipeline) conda install -c stephenfordham bacgenomepipeline

Enter y, when promoted to install dependenies in your terminal window.

Pip Install

Alternatively you can run the following commands:

 pip install BacGenomePipeline
 conda install -c bioconda filtlong==0.2.0
 conda install -c bioconda flye==2.8.1
 conda install -c bioconda abricate==1.0.1