Add docker + update setup

files/docker/Dockerfile

@@ -0,0 +1,44 @@
+FROM ubuntu:focal
+
+# Set up prefix for conda
+ENV CONDA_DIR=/miniconda3
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+ENV PATH=${CONDA_DIR}/bin:${PATH}
+
+# Copy environment definitions and database loading script
+COPY env/*.yml /tmp/
+
+# Install required system packages
+RUN apt-get update > /dev/null && \
+    apt-get install --no-install-recommends --yes \
+        wget bzip2 ca-certificates tree git tini zip unzip ncbi-blast+ \
+        > /dev/null && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/* && \
+    # Install conda
+    wget --no-hsts --quiet -O /tmp/miniconda.sh https://repo.anaconda.com/miniconda/Miniconda3-py39_24.4.0-0-Linux-x86_64.sh && \
+    /bin/bash /tmp/miniconda.sh -b -p ${CONDA_DIR} && \
+    rm /tmp/miniconda.sh && \
+    conda clean --tarballs --index-cache --packages --yes && \
+    find ${CONDA_DIR} -follow -type f -name '*.a' -delete && \
+    find ${CONDA_DIR} -follow -type f -name '*.pyc' -delete && \
+    conda clean --force-pkgs-dirs --all --yes  && \
+    echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> /etc/skel/.bashrc && \
+    echo ". ${CONDA_DIR}/etc/profile.d/conda.sh && conda activate base" >> ~/.bashrc && \
+    # Set a faster dependency solver and add necessary channels
+    conda config --set solver libmamba && \
+    conda config --add channels conda-forge && \
+    conda config --add channels bioconda && \
+    conda update --quiet --yes --all && \
+    # Create environments
+    find /tmp/ -name '*.yml' | xargs -I {} conda env create --quiet --yes --file {} && \
+    # Clean up
+    conda clean --quiet --yes -all && \
+    rm /tmp/*.yml
+
+# Find this file here: https://zenodo.org/records/11374283
+ADD panworkshop-databases.tgz /
+
+WORKDIR /root
+ENTRYPOINT ["tini", "--"]
+CMD [ "/bin/bash" ]