FROM python:3.8.20-bullseye



RUN apt-get update -y && apt-get upgrade -y && \
    apt-get install git wget ncbi-blast+-legacy mafft build-essential vim -y


# EukPhylo installation
# Tested on: RUN git clone -b patch-1 https://github.com/DLBPointon/EukPhylo.git

# Install python dependencies
RUN pip install biopython==1.75 ete3==3.1.2 tqdm==4.66.4 six==1.17.0

RUN git clone -b Docker https://github.com/Katzlab/EukPhylo.git


# Install dependencies
RUN apt-get update && apt-get install -y \
    unzip \
    cmake \
    gcc \
    g++ \
    libomp-dev \
    libboost-all-dev \
    libeigen3-dev \
    && rm -rf /var/lib/apt/lists/*

# Clone IQ-TREE 2 repository with submodules and compile it
RUN git clone --recursive https://github.com/iqtree/iqtree2.git && \
    cd iqtree2 && \
    git checkout v2.4.0 && \
    mkdir build && cd build && \
    cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ .. && \
    make -j$(nproc) && \
    make install && \
    cd ../.. && rm -rf iqtree2


# VSEARCH installation
RUN wget https://github.com/torognes/vsearch/releases/download/v2.21.0/vsearch-2.21.0-linux-aarch64.tar.gz && \
    tar xzf vsearch-2.21.0-linux-aarch64.tar.gz && \
    mv vsearch-2.21.0-linux-aarch64 /usr/local/vsearch && \
    ln -s /usr/local/vsearch/bin/vsearch /usr/local/bin/vsearch

# Guidance installation
RUN mkdir guidance && \
    wget https://taux.evolseq.net/guidance/static/download/guidance.v2.02.tar.gz && \
    tar -xzvf guidance.v2.02.tar.gz -C guidance --no-same-owner && \
    cd guidance/guidance.v2.02 && make

# Guidance bio perl dependency
RUN apt-get update && apt-get install -y cpanminus && \
    cpanm Bio::Perl

# Clean the container
RUN rm -rf vsearch-2.21.0-linux-aarch64.tar.gz guidance.v2.02.tar.gz 


# Download and compile TrimAl from source
RUN wget -O trimal-1.5.0.zip https://github.com/inab/trimal/archive/refs/tags/v1.5.0.zip && \
    unzip trimal-1.5.0.zip && \
    cd trimal-1.5.0/source && \
    make && \
    mkdir -p /usr/local/trimal && \
    cp trimal /usr/local/trimal/ && \
    ln -s /usr/local/trimal/trimal /usr/local/bin/trimal && \
    rm -rf /trimal-1.5.0.zip /trimal-1.5.0

# Install FastTree
RUN wget http://www.microbesonline.org/fasttree/FastTree && \
    chmod +x FastTree && \
    mv FastTree /usr/local/bin/


# Add executables to path
ENV PATH="$PATH:/iqtree/bin/iqtree:/usr/local/vsearch/bin/vsearch:/usr/local/trimal/trimal:/usr/local/bin"

# Change executable permissions on wrapper script
RUN ["chmod", "+x", "/EukPhylo/PTL2/run_eukphylo.sh"]

# Change executable permissions on guidance
RUN ["chmod", "+x", "/guidance/guidance.v2.02/www/Guidance/guidance.pl"]

# Change entrypoint on execution of the container
ENTRYPOINT ["bash","/EukPhylo/PTL2/run_eukphylo.sh"]