Dockerfile.compbio

FROM temp

LABEL maintainer="Joshua L. Phillips <https://www.cs.mtsu.edu/~jphillips/>"

# Install as user
USER $NB_UID

# Qiime2
RUN wget https://data.qiime2.org/distro/core/qiime2-2023.5-py38-linux-conda.yml && \
    mamba env create -n qiime2-2023.5 --file qiime2-2023.5-py38-linux-conda.yml  && \
    rm qiime2-2023.5-py38-linux-conda.yml
SHELL ["mamba", "run", "-n", "qiime2-2023.5", "/bin/bash", "-o", "pipefail", "-c"]
RUN python -m ipykernel install --name qiime2-2023.5 --prefix /opt/conda --display-name "Python 3 (Qiime2)"
SHELL ["/bin/bash", "-o", "pipefail", "-c"]

# Dada2
RUN R -e "install.packages('BiocManager',dependencies=TRUE, repos='http://cran.rstudio.com/')" && \
    R -e "BiocManager::install('dada2')" 

# Other tools... (some should probably be merged above instead)
RUN R -e "BiocManager::install('phyloseq')"

# Cleanup - not very thorough... needs revision
RUN fix-permissions "${CONDA_DIR}" && \
    fix-permissions "/home/${NB_USER}" && \
    rm -rf .npm .cache/yarn