rebar

Install

Direct

Linux

wget -O rebar https://github.com/phac-nml/rebar/releases/latest/download/rebar-x86_64-unknown-linux-musl
./rebar --help

macOS

wget -O rebar https://github.com/phac-nml/rebar/releases/latest/download/rebar-x86_64-apple-darwin
./rebar --help

Windows

wget "https://github.com/phac-nml/rebar/releases/latest/download/rebar-x86_64-pc-windows-gnu.exe" -OutFile rebar.exe
.\rebar.exe --help

Conda

conda create -c bioconda -n rebar rebar
conda activate rebar
rebar --help

Docker

GitHub Release

1. Download and load the Docker image from the releases page.

    wget -O rebar-docker.tar https://github.com/phac-nml/rebar/releases/latest/download/rebar-docker.tar
    docker load --input rebar-docker.tar
   

2. Run the image.

    docker run -v .:/rebar ghcr.io/phac-nml/rebar:latest \
    rebar --help
   

   TIP: Use -v .:/rebar to connect your local directory (.) to the docker image. That way when you run rebar dataset download, it will download permanently onto your system, not temporarily inside the image.

GitHub Container Registry

At the moment (2023-12-04), the Github Container Registry is locked to ‘private’. Only phac-nml members can access. We are working on this!

1. Authenticate with the GitHub Container Registry.

    export GITHUB_USERNAME='<Github Username>'
    export GITHUB_TOKEN='<Github Personal Access Token>'
    echo $GITHUB_TOKEN | docker login ghcr.io -u $GITHUB_USERNAME --password-stdin
   

2. Run the image.

    docker run -v .:/rebar ghcr.io/phac-nml/rebar:latest \
    rebar --help
   

Singularity

GitHub Release

1. Download and build a singularity image from the docker image.

    wget -O rebar-docker.tar https://github.com/phac-nml/rebar/releases/latest/download/rebar-docker.tar
    singularity build rebar_latest.sif docker-archive://rebar-docker.tar
   

2. Run the image

    singularity run --home $(pwd) rebar_latest.sif \
    rebar --help
   

   Tip: Use --home $(pwd) to have rebar run in your current working directory.

Container Registry

At the moment (2023-12-04), the Github Container Registry is locked to ‘private’. Only phac-nml members can access. We are working on this!

1. Download the image from the GitHub Container Registry.

    export SINGULARITY_DOCKER_USERNAME='<Github Username>'
    export SINGULARITY_DOCKER_PASSWORD='<Github Personal Access Token>'
    singularity pull docker://ghcr.io/phac-nml/rebar:latest
   

2. Run the image

    singularity run --home $(pwd) rebar_latest.sif \
    rebar --help
   

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