namzoo/circle_finder repository overview

# Pull base image
FROM phusion/baseimage:master

# Install dependencies
RUN add-apt-repository ppa:deadsnakes/ppa
RUN apt-get update && \
    DEBIAN_FRONTEND=noninteractive apt-get install --assume-yes \
    libbz2-dev \
    build-essential \
    curl \
    default-jre \
    default-jdk \
    openjdk-8-jdk \
    git \
    libcommons-math3-java \
    libcurl4-gnutls-dev \ 
    libjbzip2-java \
    liblua5.1-0-dev \
    libpng-dev \
    libssl-dev \
    libtbb2 \
    libtbb-dev \
    lua-filesystem-dev \
    lua-lpeg-dev \
    lua-md5-dev \
    libexpat1-dev \
    libtre-dev \
    libcairo2-dev \
    libpango1.0-dev \
    libsqlite3-dev \
    libbam-dev \
    libxml2-dev \
    openssl \
    perl \
    pigz=2.4-1 \
    software-properties-common \
    python3.8 \
    python3-pip \
    python3-dev \
    build-essential \
    rustc \
    liblzma-dev \
    wget \
    zlib1g \
    zlib1g-dev \
    unzip \
    parallel


# Install bedtools
RUN DEBIAN_FRONTEND=noninteractive apt-get install --assume-yes \
    ant \
    bedtools>=2.29.2 

# Install samtools
WORKDIR /home/src/
RUN wget https://github.com/samtools/samtools/releases/download/1.19.2/samtools-1.19.2.tar.bz2 && \
    tar xf samtools-1.19.2.tar.bz2&& \
    cd /home/src/samtools-1.19.2 && \
    ./configure && \
    make && \
    make install && \
    ln -s /home/src/samtools-1.19.2/samtools /usr/bin/

# Install bowtie2
WORKDIR /home/src/
RUN wget -O bowtie2-2.4.2-source.zip 'https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.4.2/bowtie2-2.4.2-source.zip?ts=gAAAAABgfxZxKMUjBU0A0XjfO55q36KUoO9RRemjzTT_WCDpSSZCy8NtKrFODKV4xS_135KTiIdnBSaqmvHuQw9l6nqM2EULvw%3D%3D&r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.4.2%2Fbowtie2-2.4.2-source.zip%2Fdownload' && \
    unzip bowtie2-2.4.2-source.zip && \
    cd /home/src/bowtie2-2.4.2 && \
    make && \
    make install && \
    ln -s /home/src/bowtie2-2.4.2/bowtie2 /usr/bin/

# Install samblaster
WORKDIR /home/tools/
RUN git clone https://github.com/GregoryFaust/samblaster.git && \
    cd /home/tools/samblaster && \
    make && \
    ln -s /home/tools/samblaster/samblaster /usr/bin/

# Install bwa
WORKDIR /home/src/
RUN wget -O bwa-0.7.17.tar.bz2  'https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2?ts=gAAAAABgfZHQ5GyuWr5rjuP8wYOC1ueJsyJD3qN-MfiwKeN3jxzRMWGU1eUfKvYzteg86k_UeLBYZTRRm1deDQaokXbPaevHYw%3D%3D&r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbio-bwa%2Ffiles%2Flatest%2Fdownload' && \
    tar xf bwa-0.7.17.tar.bz2 && \
    cd /home/src/bwa-0.7.17 && \
    make && \
    ln -s /home/src/bwa-0.7.17/bwa /usr/bin/

# Git clone the "Circle_finder" repository
WORKDIR /home/
RUN git clone https://github.com/pk7zuva/Circle_finder.git

# Make python3 default
RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 10

# Define default command
WORKDIR /home/
CMD ["/bin/bash"]

# Clean up APT when done.
RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*