Installation

Uses these steps to install MetaGenePipe:

Clone the repository

git clone https://github.com/ParkvilleData/MetaGenePipe.git
cd MetaGenePipe

MetaGenePipe requires Java, Singularity, and other dependencies to run. See below for instructions.

Java

Ensure you have Java installed (at least version 1.8 or higher). If not, follow the instructions for the relevant operating system here: https://www.java.com/en/download/help/download_options.html

If running on Spartan (the University of Melbourne HPC cluster), Java is already installed. To load Java, you can use:

module load java

Singularity

Ensure you have Singularity installed (version 3.6.3 or higher). If not, follow the instructions for the relevant operating system here: https://docs.sylabs.io/guides/3.0/user-guide/installation.html

If running on Spartan (the University of Melbourne HPC cluster), Singularity is already installed. To load Singularity, you can use:

module load singularity/3.6.3

Other Dependencies

Other necessary dependencies and databases can be downloaded using the setup script in the project directory. It requires that python (>=3.5) is available:

python3 setup.py --hmmer_kegg prokaryote --singularity y --sprott y --blast mito --cromwell y

This takes about half an hour (due to bandwidth limitations for the KEGG FTP server).

Test that the Singularity container is working with the following command:

singularity run metagenepipe_v2.sif megahit --help

If the help description for megahit displays then the Singularity container can be used with MetaGenePipe.