Dockerfile

FROM continuumio/miniconda3:4.7.10
ENV ANVIO_VERSION "6.1_master"

RUN conda config --env --add channels conda-forge
RUN conda config --env --add channels bioconda
RUN conda create -n anvioenv python=3.6

# Activate environment
ENV PATH /opt/conda/envs/anvioenv/bin:$PATH
ENV CONDA_DEFAULT_ENV anvioenv
ENV CONDA_PREFIX /opt/conda/envs/anvioenv

RUN echo "conda activate anvioenv" >> ~/.bashrc
SHELL ["/bin/bash", "-c"]

RUN conda install -y conda-build

COPY conda-recipe /tmp/conda-recipe
RUN conda-build /tmp/conda-recipe/anvio-minimal && conda-build /tmp/conda-recipe/anvio

# Install Anvi'o
RUN conda index /opt/conda/envs/anvioenv/conda-bld/
RUN conda install -c file:///opt/conda/envs/anvioenv/conda-bld/ anvio-minimal=$ANVIO_VERSION
RUN conda install -c file:///opt/conda/envs/anvioenv/conda-bld/ anvio=$ANVIO_VERSION

# Install METABAT and DAS_TOOL
RUN conda install metabat2 das_tool

# Install CONCOCT
RUN apt-get update && apt-get install -qq build-essential libgsl0-dev bedtools mummer samtools perl libssl-dev
RUN pip install https://github.com/BinPro/CONCOCT/archive/1.1.0.tar.gz

# Install BINSANITY
RUN pip install git+https://github.com/edgraham/BinSanity.git

# Install MAXBIN2 (installing fraggenescan will require cpanm, and we also need IDBA-UD)
RUN conda install -c bioconda perl-app-cpanminus
RUN cpanm --self-upgrade --sudo
RUN conda install -c bioconda idba
RUN cd /opt && wget https://downloads.sourceforge.net/project/fraggenescan/FragGeneScan1.31.tar.gz && tar zxf FragGeneScan1.31.tar.gz && cd FragGeneScan1.31 && make clean && make
RUN cpanm install LWP::Simple
ENV PERL5LIB /opt/conda/envs/anvioenv/lib/5.26.2/:/opt/conda/envs/anvioenv/lib/site_perl/5.26.2/:$PERL5LIB
RUN cd /opt && wget https://downloads.sourceforge.net/project/maxbin2/MaxBin-2.2.7.tar.gz && tar zxf MaxBin-2.2.7.tar.gz && cd MaxBin-2.2.7/src && make
RUN echo 'export PATH=/opt/FragGeneScan1.31:$PATH' >> ~/.bashrc
RUN echo 'export PATH=/opt/MaxBin-2.2.7:$PATH' >> ~/.bashrc

# Install some helper tools
RUN pip install virtualenv
RUN apt-get install vim util-linux -yy

# Setup the environment
RUN echo "export PS1=\"\[\e[0m\e[47m\e[1;30m\] :: anvi'o v$ANVIO_VERSION :: \[\e[0m\e[0m \[\e[1;34m\]\]\w\[\e[m\] \[\e[1;32m\]>>>\[\e[m\] \[\e[0m\]\"" >> /root/.bashrc

CMD /bin/bash -l