Installation & Dependencies - jacksonhturner/orthogarden GitHub Wiki

Dependencies

Orthogarden is built for LINUX-based systems and relies on Nextflow and Apptainer (FKA Singularity). Both must be installed and available in your working environment prior to use.

Nextflow installation routes:

• Nextflow quick install guide (requires Java)
• Nextflow conda image (requires Anaconda)

Assuming your machine is set up with the appropriate prerequisite Java version and you have permissions to do so, installing nextflow might be as easy as:

cd ~
curl -s https://get.nextflow.io | bash
chmod +x nextflow

Apptainer installation routes:

• Apptainer quick install
• Apptainer binary See "Install unprivileged from pre-built binaries".
• we recommend against using the conda package for singularity (v3.8.7) as it is quite dated and has been found to have unintended behaviors with Orthogarden

A possible route to installing the unprivileged version of Apptainer might go something like this on your system:

cd ~
curl -s https://raw.githubusercontent.com/apptainer/apptainer/main/tools/install-unprivileged.sh | bash -s - ~/

Installation

Orthogarden is publicly available through its github page.

git clone https://github.com/jacksonhturner/orthogarden.git

Other use notes

Running OrthoGarden on a server with robust CPU and memory is highly recommended. This software has been tested on multi-user server (RHEL 8.9; 503GB; 96 cores) and using slurm management settings on the University of Tennessee ISAAC-NG HPC.