diff --git a/docker/Dockerfile b/docker/Dockerfile index 5bc4a7b..4041d2a 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,9 +1,9 @@ # Use the official QIIME 2 image as a parent image -FROM quay.io/qiime2/core:2023.2 +FROM quay.io/qiime2/core:2023.5 # Label information LABEL maintainer="Luke Thompson" -LABEL description="Docker image to build the Tourmaline Snakemake workflow for QIIME 2 v.2023.2" +LABEL description="Docker image to build the Tourmaline Snakemake workflow for QIIME 2 v.2023.5" # Set up bash environment: aliases, colors, history RUN echo "alias cd..='cd ..'" >> ~/.bashrc @@ -29,14 +29,15 @@ RUN apt-get update -y && \ RUN pip install empress # Add conda installation dir to $PATH (instead of doing 'conda activate') -ENV PATH="/opt/conda/envs/qiime2-2023.2/bin:$PATH" +ENV PATH /opt/conda/bin:${PATH} -# This is necessary to install snakemake using conda -SHELL ["conda", "run", "-n", "qiime2-2023.2", "/bin/bash", "-c"] - -# Install snakemake and other dependencies using conda -RUN conda update -n base -c defaults conda -RUN conda install -c conda-forge -c bioconda snakemake biopython muscle clustalo tabulate -RUN conda install -c conda-forge deicode -RUN qiime dev refresh-cache -RUN conda install -c bioconda bioconductor-msa bioconductor-odseq +# Install snakemake environment +RUN /bin/bash -c "conda update -n base -c defaults conda" +RUN /bin/bash -c "conda create -y -c conda-forge -c bioconda -n snakemake snakemake snakemake-minimal --only-deps" +RUN echo "source activate snakemake" > ~/.bashrc +ENV PATH /opt/conda/envs/snakemake/bin:${PATH} + +# Install tourmaline dependencies using conda +RUN conda install -n qiime2-2023.5 -c conda-forge -c bioconda biopython muscle clustalo tabulate +RUN conda install -n qiime2-2023.5 -c conda-forge deicode +RUN conda install -n qiime2-2023.5 -c bioconda bioconductor-msa bioconductor-odseq \ No newline at end of file