Dockerfile

# syntax=docker/dockerfile:1

# FROM davidemms/orthofinder
FROM ubuntu:22.04
# ARG PYTHON_VERSION=3.10.2
# FROM python:${PYTHON_VERSION}-slim as base

# Prevents Python from writing pyc files.
# ENV PYTHONDONTWRITEBYTECODE=1
ENV DEBIAN_FRONTEND=noninteractive

# Keeps Python from buffering stdout and stderr to avoid situations where
# the application crashes without emitting any logs due to buffering.
#ENV PYTHONUNBUFFERED=1

WORKDIR /app

# Download python, pip and required dependencies.
RUN apt-get update && apt-get install -y \
    wget \
    unzip \
    gffread \
    sudo \
    g++ \
    make \
    git

RUN apt-get install -y python3

RUN ln -s /usr/bin/python3 /usr/bin/python
RUN apt install -y python3-pip
RUN --mount=type=cache,target=/root/.cache/pip \
    --mount=type=bind,source=./requirements.txt,target=./requirements.txt \
    pip install -r requirements.txt

# configure the MatPlotLib tmp directory
ENV MPLCONFIGDIR=/tmp/matplotlib

# Include OrthoFinder in the image
RUN wget https://github.com/davidemms/OrthoFinder/releases/download/2.5.5/OrthoFinder.tar.gz && \
    tar xzvf OrthoFinder.tar.gz && \
    rm OrthoFinder.tar.gz

# Include KaKs_Calculator in the image
RUN wget https://ngdc.cncb.ac.cn/biocode/tools/1/releases/3.0/file/download?filename=KaKs_Calculator3.0.zip -O KaKs_Calculator3.0.zip && \
    unzip KaKs_Calculator3.0.zip && \
    rm KaKs_Calculator3.0.zip && \ 
    cd KaKs_Calculator3.0/src && \
    make

# Include paraAT in the image
RUN wget https://download.cncb.ac.cn/bigd/tools/ParaAT2.0.tar.gz && \
    tar -xf ParaAT2.0.tar.gz && \
    rm ParaAT2.0.tar.gz

RUN apt-get install -y locate libc6 muscle

#RUN apt-get install gawk bison gcc make wget tar -y && \
#    wget -c https://ftp.gnu.org/gnu/glibc/glibc-2.35.tar.gz && \
#    tar -zxvf glibc-2.35.tar.gz && cd glibc-2.35 && \
#    mkdir glibc-build && cd glibc-build && \
#    ../configure --prefix=/opt/glibc && \
#    make && \
#    make install


#RUN adduser \
#    --disabled-password \
#    --gecos "" \
#    --home "/nonexistent" \
#    --shell "/sbin/nologin" \
#    --no-create-home \
#    --uid "${UID}" \
#    appuser
#
#USER appuser

# Copy the source code into the container.
# RUN git clone --depth 1 https://github.com/cl3mente/PlantPath2023.git

COPY . .

RUN cp -f /app/ParaAT.pl /app/ParaAT2.0/ParaAT.pl

ENV PATH=$PATH:/app/KaKs_Calculator3.0/src:/app/ParaAT2.0:/app/OrthoFinder

RUN mkdir input

VOLUME /app/input

# CMD python HGT.py -i /data/bioinf2023/PlantPath2023/genomeANDgff -OFr /data/bioinf2023/PlantPath2023/genomeANDgff/results/prot/f7b812/Results_Feb23  -v -nt 50
#ENTRYPOINT ["python","./HGT.py", "-i", "input"]