diff --git a/.github/workflows/dockerpublish.yml b/.github/workflows/dockerpublish.yml deleted file mode 100644 index 145244d..0000000 --- a/.github/workflows/dockerpublish.yml +++ /dev/null @@ -1,34 +0,0 @@ -name: Publish Docker Image - -on: - release: - types: [published] - -jobs: - main: - runs-on: ubuntu-latest - steps: - - - name: Set up QEMU - uses: docker/setup-qemu-action@v1 - - - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v1 - - - name: Login to DockerHub - uses: docker/login-action@v1 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - - - name: Build and push - id: docker_build - uses: docker/build-push-action@v2 - with: - push: true - tags: finlaymaguire/rgi:latest - build-args: | - software_version=${{ github.event.release.tag_name }} - - - name: Image digest - run: echo ${{ steps.docker_build.outputs.digest }} diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index 8ac777f..0000000 --- a/Dockerfile +++ /dev/null @@ -1,40 +0,0 @@ -# base image (stripped down ubuntu for Docker) -FROM continuumio/miniconda3 - -# metadata -LABEL base.image="miniconda3" -LABEL version="2" -LABEL software="RGI" -LABEL description="Tool to identify resistance genes using the CARD database" -LABEL website="https://card.mcmaster.ca/" -LABEL documentation="https://github.com/arpcard/rgi/blob/master/README.rst" -LABEL license="https://github.com/arpcard/rgi/blob/master/LICENSE" -LABEL tags="Genomics" - -# maintainer -MAINTAINER Finlay Maguire - -# get some system essentials -RUN apt-get update && apt-get install -y wget && conda init bash - -# get latest version of the repo -RUN git clone https://github.com/arpcard/rgi -WORKDIR rgi - -# install all dependencies matching bioconda package meta.yml -RUN conda env create -f conda_env.yml - -# configure conda shell -SHELL ["conda", "run", "-n", "rgi", "/bin/bash", "-c"] - -# install RGI in the repo itself -RUN pip install . - -# install databases -RUN rgi auto_load - -# Move to workdir -WORKDIR /data - -# set rgi executable as cmd to allow overriding -ENTRYPOINT ["conda", "run", "-n", "rgi"] diff --git a/README.rst b/README.rst index 6f0ca65..a79fee3 100644 --- a/README.rst +++ b/README.rst @@ -211,34 +211,22 @@ Remove RGI package: Install RGI using Docker/Singularity ------------------------------------ -RGI is available via dockerhub or biocontainers full installed with all +RGI is available via biocontainers full installed with all databases appropriately loaded. Install `docker `_ on your system if not already available -- Pull the Docker container from dockerhub (built from Dockerfile in repository) or biocontainers (built from Conda package). +- Pull the Docker container from biocontainers (built from Conda package at https://quay.io/repository/biocontainers/rgi?tab=tags&tag=latest). .. code-block:: sh - docker pull finlaymaguire/rgi:latest + docker pull quay.io/biocontainers/rgi:6.0.3--pyha8f3691_0 - Or +- RGI can be executed from the container as follows: .. code-block:: sh - docker pull quay.io/biocontainers/rgi:5.1.1--py_0 - -- RGI can be executed from the containers as follows: - - .. code-block:: sh - - docker run -v $PWD:/data finlaymaguire/rgi rgi -h - - Or - - .. code-block:: sh - - docker run -v $PWD:/data quay.io/biocontainers/rgi:5.1.1--py_0 rgi -h + docker run -v $PWD:/data quay.io/biocontainers/rgi:6.0.3--pyha8f3691_0 rgi -h Install Development Version