Installation

Installation for workstation use

TRIBES requires a 64-bit version of Linux, MacOS or Windows 10.

Windows Subsystem for Linux (WSL)

To run TRIBES on Windows 10, first install Ubuntu from the Microsoft Store.

Then open the Ubuntu app from the Start menu.

Miniconda

TRIBES has a list of dependencies required to be installed prior to running the analysis pipeline. For this, we use Miniconda.

Install miniconda (3.7 or 2.7) from https://docs.conda.io/en/latest/miniconda.html:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

Download TRIBES

Download the latest release of TRIBES from https://github.com/aehrc/TRIBES/releases and extract it to your selected directory.

Alternatively you can clone the most recent (unstable) version from github:

git clone https://github.com/aehrc/TRIBES.git

Installing TRIBES

Go to the TRIBES installation directory.

Install dependencies (requires about 500 MB for software packages):

./setup/install-with-conda.sh

This will create an conda environment named tribes and install all required dependencies, as well as create the appropriate TRIBES configuration file at ~/.tribesrc

To check the installation run:

./tribes

This should display among others usage info.

After you install TRIBES, return to Testing installation on example dataset to test the installation on example data.

Manual installation

TRIBES is implemented as a snakemake pipeline and relies a number of bioinformatics tools for processing, such as bcftools, bgzip, tabix, vcftools, germline, beagle as well as a number of python an R packages.

The complete list of dependencies and their required (minimal) versions can be inferred from the conda environment file at: setup/environment.yaml

They can be installed using the OS specific way (e.g. using apt or yum on Linxu or brew on MacOS)

In addition TRIBES requires tribes.tools R packages which can be installed from sources with:

Rscript --vanilla -e "install.packages('R/tribes.tools',repos=NULL)"

Installation on HPC Cluster

snakemake and thus TRIBES can run on HPC clusters (for example with slurm).

An example setup for CSIRO HPC cluster is descibed in README-CSIRO.md and can be used as a guide to configure TRIBES on other clusters.

For more information on running snakemake on HPC clusters please check the snakemake documentation https://snakemake.readthedocs.io/en/stable/