Merge pull request #109 from aomlomics/qiime2-2023.5

Qiime2 2023.5

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