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Installation

Source: vignettes/installation.qmd

There are several ways to install {nemo}:

R

Using {remotes} directly from GitHub:

install.packages("remotes")
remotes::install_github("umccr/nemo") # latest main commit
remotes::install_github("umccr/nemo@v0.0.1") # released version

Conda

conda-versionconda-latest

The conda package is available from the umccr channel at https://anaconda.org/umccr/r-nemo.

conda create \
  -n nemo_env \
  -c umccr -c conda-forge \
  r-nemo==0.0.1

conda activate nemo_env

Pixi

If you use Pixi, you can create a new isolated environment with the deployed conda package:

pixi init -c umccr -c conda-forge ./tidy_env
cd ./tidy_env
pixi add r-nemo==0.0.1

Then you can create a task to run the nemo.R CLI script:

pixi task add nemo "nemo.R"
pixi run nemo --help

Or activate the environment and use nemo directly in an R environment:

pixi shell
R