sstevens/checkm repository overview

FROM ubuntu:16.04

# Installing all dependancies
RUN apt-get update && apt-get install -y \ 
        unzip \ 
        make \
        wget \ 
        build-essential \
        python \
        python-pip


# prodigal
RUN mkdir /checkm-deps && \
    cd /checkm-deps && wget https://github.com/hyattpd/Prodigal/releases/download/v2.6.3/prodigal.linux && \
    mv prodigal.linux /usr/local/bin/prodigal && chmod 755 /usr/local/bin/prodigal
# hmmer
RUN cd /checkm-deps && wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz && \
    tar -xvzf hmmer-3.1b2-linux-intel-x86_64.tar.gz && \
    cd hmmer-3.1b2-linux-intel-x86_64 && ./configure &&  \
    make && make install
# pplacer
RUN cd /checkm-deps && wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip && \
    unzip pplacer-linux-v1.1.alpha19.zip && \
    cp pplacer-Linux-v1.1.alpha19/pplacer /usr/local/bin/ && \
    cp pplacer-Linux-v1.1.alpha19/guppy /usr/local/bin/ && \
    cp pplacer-Linux-v1.1.alpha19/rppr /usr/local/bin/
# checkm 
RUN pip install numpy && pip install checkm-genome
## checkm data 
RUN cd / && mkdir checkm-data && cd checkm-data && \
    wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz && \
    tar -xvzf checkm_data_2015_01_16.tar.gz

#set root w/command `checkm data setRoot /checkm-data`