#FROM ubuntu:20.04
FROM continuumio/miniconda3:24.3.0-0

WORKDIR /motif-search/

ENV DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC

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

COPY ./meme-5.5.4.tar.gz  .
# RUN wget https://meme-suite.org/meme/meme-software/5.5.4/meme-5.5.4.tar.gz
RUN tar -zxf ./meme-5.5.4.tar.gz 
RUN rm meme-5.5.4.tar.gz 

COPY entrypoint.sh . 

RUN apt update \
    && apt-get install -y --no-install-recommends \
    wget \
	build-essential \
    ca-certificates \
    curl \
    imagemagick \
    libexpat1-dev \
    libxml2-dev \
	libxslt1-dev \
	libgs-dev \
    libgd-dev \
	#libexslt1-dev \
    python3 \
    zlib1g-dev \
	perl \
	libxml-simple-perl \
	libxml-libxml-perl \
	libxml-parser-perl \
	libhtml-template-compiled-perl \
    libxml-opml-simplegen-perl \
    libxml-libxml-debugging-perl \
    && apt-get clean 
  
# Install meme-chip
RUN cd meme-5.5.4 && \
    ./configure --prefix=/motif-search/meme --with-url="http://meme-suite.org" --enable-build-libxml2 --enable-build-libxslt && \
    make && \
    # make test && \
    make install && \
	export PATH=/motif-search/meme/bin/:/motif-search/meme/libexec/meme-5.5.4:$PATH && \
    meme -version && \
    meme-chip --version && \
    spamo --version && \
    centrimo --version && \
    # apt-get remove -y build-essential libxml2 libxml2-dev libxslt1-dev && \
    apt-get clean

# Enable the use of bash-specific conda commands in the layer.
RUN eval "$(conda shell.bash hook)" && \
    chmod +x entrypoint.sh && \
    #conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=2.7.12 pip=9.0.1 && \
    conda create -y -c bioconda -c conda-forge -c defaults -n motifSearch python=3.6.1 && \
	conda activate motifSearch && \
    python --version && \
    # Install pandas and numpy.
    pip install numpy==1.12.1 && \
    pip install pandas==0.20.1 && \
    # Install BEDTools 2.26 .0
    conda install -y --solver=libmamba -c bioconda bedtools=2.26.0 && \
    bedtools --version && \
    conda clean -y --all && \
    conda deactivate 

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