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/