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 20.04; macOS has not been tested yet)
Conda (tested with conda 22.11.1)
Mamba (tested with mamba 1.3.0)
Singularity (tested with singularity 3.8.6; not required if you have root permissions on the machine you would like to install ZARP-cli on; in that case, choose one of the .root. environment file flavors below)

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

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 four different environment files. Use this decision matrix to pick the most suitable one for you:

I have root privileges on the machine	I want to run pre-packaged tests	Environment file to use
		`install/environment.yml`
		`install/environment.root.yml`
		`install/environment.dev.yml`
		`install/environment.dev.root.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:

mamba 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.