Dockerfile

FROM debian:stable
MAINTAINER Nathan Olson "https://github.com/nate-d-olson"
# edited by Adrian Fritz Adrian.Fritz@Helmholtz-HZI.de

# Setup a base system
ENV DEBIAN_FRONTEND noninteractive

RUN apt-get update
RUN apt-get install -y -q   \
                            git \
                            build-essential \
                            wget \
                            unzip \
                            zlib1g-dev \
                            libbz2-dev \
                            libncurses5-dev \
                            libarchive-dev \
                            libexpat1-dev \
                            openjdk-7-jdk \
                            openjdk-7-jre \
                            r-base \
                            r-base-dev \
                            r-recommended \
                            python-setuptools \
                            python-pip \
                            perl

RUN echo 'options(repos = list(CRAN = "http://cran.rstudio.com/"))' >> /etc/R/Rprofile.site

# install bowtie2
RUN wget http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.2/bowtie2-2.2.2-linux-x86_64.zip;\
    unzip bowtie2-2.2.2-linux-x86_64.zip && rm -rf bowtie2-2.2.2-linux-x86_64.zip;\
    ln -s `pwd`/bowtie*/bowtie* /usr/local/bin

# install htslib samtools
RUN wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2;\
    tar -xaf samtools-1.2.tar.bz2 && rm -rf samtools-1.2.tar.bz2 ;\
    cd samtools-1.2;\
    make && ln -f -s `pwd`/* /usr/local/bin/ && cd ../

# install bedtools
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.24.0/bedtools-2.24.0.tar.gz;\
    tar -xaf bedtools-2.24.0.tar.gz && rm -rf bedtools-2.24.0.tar.gz ;\
    cd bedtools2;\
    make && ln -f -s `pwd`/bin/* /usr/local/bin/ && cd ../

# install Perl modules for REAPR
RUN apt-get install -y cpanminus
RUN cpanm -v JSON File::Basename File::Copy File::Spec File::Spec::Link Getopt::Long List::Util

# instal REAPR
RUN wget ftp://ftp.sanger.ac.uk/pub/resources/software/reapr/Reapr_1.0.18.tar.gz;\
    tar -xaf Reapr_1.0.18.tar.gz && rm -rf Reapr_1.0.18.tar.gz;\
    cd Reapr_1.0.18;\
    ./install.sh && ln -f -s `pwd`/reapr /usr/local/bin/ && cd ../

# install VALET
RUN apt-get install -y -q python-numpy python-scipy
RUN git clone https://github.com/marbl/VALET.git
RUN ln -s VALET/src/py/valet.py valet
RUN chmod +x valet

ENV CONVERT https://github.com/bronze1man/yaml2json/raw/master/builds/linux_386/yaml2json
# download yaml2json and make it executable
RUN cd /usr/local/bin && wget ${CONVERT} && chmod 700 yaml2json

ENV JQ http://stedolan.github.io/jq/download/linux64/jq
# download jq and make it executable
RUN cd /usr/local/bin && wget --quiet ${JQ} && chmod 700 jq

# Locations for biobox file validator
ENV VALIDATOR /bbx/validator/
ENV BASE_URL https://s3-us-west-1.amazonaws.com/bioboxes-tools/validate-biobox-file
ENV VERSION  0.x.y
RUN mkdir -p ${VALIDATOR}

# download the validate-biobox-file binary and extract it to the directory $VALIDATOR
RUN wget \
      --quiet \
      --output-document -\
      ${BASE_URL}/${VERSION}/validate-biobox-file.tar.xz \
    | tar xJf - \
      --directory ${VALIDATOR} \
      --strip-components=1

ENV PATH ${PATH}:${VALIDATOR}

# Add Taskfile to /
ADD Taskfile /

ADD validate /usr/local/bin/

ADD schema.yaml /

ADD unshuffle.pl /

ENTRYPOINT ["validate"]