FROM continuumio/miniconda3:24.3.0-0

LABEL IMAGE="chipseq-analysis-motifSearch" \
    IMAGE_VERSION="1.0.0" \
    AUTHORS="Felix Perez,Peng Lian" \
    EMAIL="biohpc-help@utsouthwestern.edu"

WORKDIR /motif-search/

# Environment variables for the campus proxy.
ENV http_proxy="http://proxy.swmed.edu:3128" \
    https_proxy="http://proxy.swmed.edu:3128"


# Original module load order:
# module load python/3.6.1-2-anaconda
# module load meme/4.11.1-gcc-openmpi
# module load bedtools/2.26.0


COPY entrypoint.sh .

RUN eval "$(conda shell.bash hook)" && \
    conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=2.7.12 pip=9.0.1 && \
    echo "python ==2.7.12" >> /opt/conda/envs/motifSearch/conda-meta/pinned && \
    conda activate motifSearch && \
    # Install pandas and numpy.
    pip install numpy==1.12.1 && \
    pip install pandas==0.20.1 && \
    # Install MEME 4.11.1
    conda install -y --solver=libmamba -c conda-forge -c bioconda meme=4.11.1 && \
    meme -version && \
    # Install BEDTools 2.26.0
    conda install -y --solver=libmamba -c bioconda bedtools=2.26.0 && \
    bedtools --version && \
    # The stringi installation below solves a dependency issue encountered when DREME is used (meme-4.11.1)
    conda install -y --solver=libmamba -c conda-forge r-stringi=1.2.4 && \
    conda deactivate

RUN eval "$(conda shell.bash hook)" && \
    # Create a Python 3.6.1 conda environment and initialize its use.
    conda create -y -c bioconda -c defaults -c conda-forge -n py361 python=3.6.1 && \
    echo "python ==3.6.1" >> /opt/conda/envs/py361/conda-meta/pinned && \
    conda update conda -y && \
    conda activate py361 && \
    # Install the versions of numpy and pandas required for further software installs.
    pip install numpy==1.12.1 && \
    pip install pandas==0.20.1 && \
    conda deactivate && \
    ln -s /opt/conda/envs/py361/bin/python3 /opt/conda/envs/motifSearch/bin/python3

RUN chmod +x entrypoint.sh

ENTRYPOINT ["/motif-search/entrypoint.sh"]