To run AMR++, you will need the following tool installed on your server or local machine.
- Anaconda or miniconda (Required)
- Visit this website for further information: https://docs.anaconda.com/anaconda/install/
NOTE: If you choose not to install anaconda, you will need to download each of the required dependencies and add the executable paths to your .bashrc file to run the pipeline. A list of these dependencies can be found in the Dependencies section of this document.
If anaconda or docker is not available to you, in addition to installing the listed bioinformatic tool dependencies, you'll need to install the following tools:
- Java 7+ (Required)
- Nextflow (Required)
Another option is to use singularity:
singularity pull docker://enriquedoster/amrplusplus:latest nextflow run main_AMR++.nf -profile local --pipeline demo -with-singularity amrplusplus_latest.sif