concoct_dockerfile

#FROM continuumio/anaconda3
#version 1.0.0: 

FROM ubuntu:22.04
MAINTAINER Billy Law

ENV TZ=America/Canada
ENV DEBIAN_FRONTEND=noninteractive



RUN apt-get update \
&& apt-get -y install wget \
&& apt-get -y install unzip \
&& apt-get -y install g++ \
&& apt-get -y install gcc \
&& apt-get -y install make \
&& apt-get install -y valgrind \
&& apt-get install -y heaptrack \
&& apt-get install -y nano \
&& apt-get install -y libgsl-dev \
&& apt-get install -y libncurses5-dev \
&& apt-get install -y libbz2-dev \
&& apt-get install -y liblzma-dev \
&& apt-get install -y libopenblas-dev

RUN apt-get update --fix-missing \
&& apt-get install -y software-properties-common
RUN add-apt-repository ppa:deadsnakes/ppa


RUN apt-get update \
&& apt-get install -y python3
RUN apt-get install -y python3-pip
RUN echo 'alias python="python3"' >> ~/.bashrc
#this line is necessary for concoct due to some annoying artifact.
RUN ln -s /usr/bin/python3.5 /usr/bin/python


ENV CONDA_DIR="/opt/conda"
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda
# Put conda in path so we can use conda activate
ENV PATH=$CONDA_DIR/bin:$PATH

RUN conda config --add channels defaults \
&& conda config --add channels conda-forge \
&& conda config --add channels bioconda \
&& conda config --add channels ursky 

RUn pip install --upgrade pip
RUN pip install cryptography
RUN apt-get install -y libffi-dev
RUN pip install pyopenssl --upgrade

#RUN conda install -y concoct
RUN conda install -y pandas
RUN conda update -n base -c conda-forge conda
RUN conda install -y numpy
RUN conda install -y scipy 
RUN conda install -y cython 
RUN conda install -y scikit-learn
RUN conda install -y biopython


WORKDIR /quackers_tools
RUN wget https://github.com/BinPro/CONCOCT/archive/refs/tags/1.1.0.zip \
&& unzip 1.1.0.zip 
#&& python CONCOCT-1.1.0/setup.py install

WORKDIR CONCOCT-1.1.0
RUN python setup.py install