Installation

Option 1: Conda

It's recommended that you create a new environment to ensure conda can correctly handle of the rosella's dependencies:

conda create -n rosella -c bioconda rosella
conda activate rosella
rosella --version

Option 2: Install manually

After cloning the repo with rust and cargo installed on your system

cd rosella
cargo install --path .

Create the conda environment

mamba env create -f rosella.yml -n rosella
mamba activate rosella
rosella --help

Requirements

Initial requirements for rosella can be downloaded using the rosella.yml:

conda env create -n rosella -f rosella.yml

Shell completion

Completion scripts for various shells e.g. BASH can be generated. For example, to install the bash completion script system-wide (this requires root privileges):

rosella shell-completion --output-file rosella --shell bash
mv rosella /etc/bash_completion.d/

It can also be installed into a user's home directory (root privileges not required):

rosella shell-completion --shell bash --output-file /dev/stdout >>~/.bash_completion

In both cases, to take effect, the terminal will likely need to be restarted. To test, type rosella rec and it should complete after pressing the TAB key.