Installation

On this page, you will find out how to install ZARP-cli on your system.

Requirements

Installation requires the following:

• Linux (tested with Ubuntu 24.04)
• Conda (tested with conda 24.11.3)
• Recommended: Apptainer (tested with apptainer 1.3.6; only required for dependency embedding strategy APPTAINER)

Other versions, especially older ones, are not guaranteed to work!

How do I install Apptainer?

Please follow the official documentation to install Apptainer (formerly Singularity) globally and configure its permissions. To test whether your Apptainer configuration is adequate, you can check whether the following commands complete without errors:

apptainer pull docker://alpine:latest
apptainer run alpine_latest.sif echo "Hello from Apptainer"

Wanna run ZARP on your HPC cluster?

ZARP should be able to run on a sufficiently powered (32+GB RAM), modern laptop for most samples. However, if you want to analyze large samples, or a large number of samples, we recommend connecting ZARP to an HPC cluster.

In that case, you will need to make sure that compatible versions of at least one of Conda and Apptainer (when using dependency embedding strategies CONDA and APPTAINER, respectively) are installed and properly configured on each machine of the cluster, including the head node(s). Reach out to your systems administrator to set this up for you.

Once Conda and/or Apptainer are set up, follow the ZARP documentation to use, create or extend the necessary Snakemake execution profiles to connect ZARP runs to your HPC cluster.

Note that ZARP-cli installs the Snakemake 8+ plugin snakemake-executor-plugin-cluster-generic required for HPC cluster execution by default.

Installation steps

1. Clone ZARP

Clone the ZARP workflow repository with:

git clone git@github.com:zavolanlab/zarp
# or: git clone https://github.com/zavolanlab/zarp.git

2. Clone ZARP-cli

Clone the ZARP-cli repository and traverse into it with:

git clone git@github.com:zavolanlab/zarp-cli.git
# or: git clone https://github.com/zavolanlab/zarp-cli.git
cd zarp-cli

3. Set up environment

In the next step, you need to install the app with its dependencies. For that purpose, there exist two different "environment files". Use this decision matrix to pick the most suitable one for you:

I want to run pre-packaged tests	Environment file to use
	install/environment.yml
	install/environment.dev.yml

To set up the environment, execute the call below, but do not forget to replace the placeholder ENVIRONMENT with the appropriate file from the table above:

conda env create -f ENVIRONMENT

4. Activate environment

Finally, activate the Conda environment with:

conda activate zarp-cli

You should now be good to go to proceed with initialization.