Dockerfile

FROM ubuntu:16.04

LABEL base.image="ubuntu:16:04"
LABEL version="1"
LABEL software="SalmonTE"
LABEL software.version="0.4"
LABEL description="An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data"
LABEL website="https://github.com/hyunhwaj/SalmonTE"
LABEL documentation="https://github.com/hyunhwaj/SalmonTE/blob/master/README.md"
LABEL license="https://github.com/hyunhwaj/SalmonTE/blob/master/LICENSE"
LABEL tags="Genomics"
LABEL maintainer="Wen-Wei Liao <wen-wei.liao@wustl.edu>, Xiaofei Wang <xiw4006@med.cornell.edu>, Andrea Sboner <ans2077@med.cornell.edu>"

ENV DEBIAN_FRONTEND noninteractive

RUN mv /etc/apt/sources.list /etc/apt/sources.list.bkp && \
    bash -c 'echo -e "deb mirror://mirrors.ubuntu.com/mirrors.txt xenial main restricted universe multiverse\n\
deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-updates main restricted universe multiverse\n\
deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-backports main restricted universe multiverse\n\
deb mirror://mirrors.ubuntu.com/mirrors.txt xenial-security main restricted universe multiverse\n\n" > /etc/apt/sources.list' && \
    cat /etc/apt/sources.list.bkp >> /etc/apt/sources.list && \
    cat /etc/apt/sources.list

RUN apt-get clean all &&  \
    apt-get update &&     \
    apt-get upgrade -y && \
    apt-get install -y    \
        autotools-dev     \
        automake          \
        cmake             \
        curl              \
        grep              \
        sed               \
        dpkg              \
        fuse              \
        git               \
        wget              \
        zip               \
        openjdk-8-jre     \
        build-essential   \
        pkg-config        \
        python            \
        python-dev        \
        python-pip        \
        bzip2             \
        ca-certificates   \
        libglib2.0-0      \
        libxext6          \
        libsm6            \
        libxrender1       \
        git               \
        mercurial         \
        subversion        \
        r-base            \
        r-base-dev        \
        libnss-sss        \
        locales           \
        zlib1g-dev &&     \
    locale-gen en_US.UTF-8 && \
    apt-get clean &&  \
    apt-get purge &&  \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh

RUN TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o "/v.*\"" | sed 's:^..\(.*\).$:\1:'` && \
    curl -L "https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb" > tini.deb && \
    dpkg -i tini.deb && \
    rm tini.deb && \
    apt-get clean

RUN mkdir /data /config

# Add user biodocker with password biodocker
RUN groupadd fuse && \
    useradd --create-home --shell /bin/bash --user-group --uid 1000 --groups sudo,fuse biodocker && \
    echo `echo "biodocker\nbiodocker\n" | passwd biodocker` && \
    chown biodocker:biodocker /data && \
    chown biodocker:biodocker /config

# give write permissions to conda folder
RUN chmod 777 -R /opt/conda/

ENV PATH=$PATH:/opt/conda/bin
ENV PATH=$PATH:/home/biodocker/bin
ENV HOME=/home/biodocker

RUN mkdir /home/biodocker/bin

RUN conda config --add channels r
RUN conda config --add channels conda-forge
RUN conda config --add channels bioconda

RUN conda upgrade conda

VOLUME ["/data", "/config"]


RUN conda install snakemake docopt pandas r
RUN conda install r-tidyverse r-scales r-writexls r-cowplot
RUN conda install bioconductor-deseq2 bioconductor-tximport

WORKDIR $HOME

COPY SalmonTE.py        $HOME/SalmonTE/
COPY SalmonTE_Stats.R   $HOME/SalmonTE/
COPY scripts/           $HOME/SalmonTE/scripts/
COPY reference/         $HOME/SalmonTE/reference/
COPY bin/               $HOME/SalmonTE/bin/
COPY test/              $HOME/SalmonTE/test/
COPY snakemake/         $HOME/SalmonTE/snakemake/
COPY example/           $HOME/SalmonTE/example/
COPY salmon/            $HOME/SalmonTE/salmon/

ENV PATH=$PATH:$HOME/SalmonTE

RUN chmod 777 $HOME

WORKDIR /data