Dockerfile.with_refs

FROM ghcr.io/iqbal-lab-org/clockwork:v0.11.3

ENV DEBIAN_FRONTEND=noninteractive
ENV LANG=C.UTF-8
ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

RUN apt-get update && apt-get install -y python2.7 zlib1g-dev wget libbz2-dev liblzma-dev bzip2 make gcc libncurses5-dev \
					 automake build-essential cmake curl gawk git gnuplot graphviz libarchive-dev libcurl4-gnutls-dev \
					 libhts-dev libncursesw5-dev libvcflib-tools libssl-dev pkg-config python3-dev python3-pip \
					 python3-setuptools r-base-core rsync unzip tabix libssl-dev openjdk-8-jdk

COPY --chmod=755 ./tools /varpipe_wgs/tools

RUN mkdir /build && cd /build &&\
    wget -O- https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2 >samtools-1.11.tar.bz2 &&\
    tar -xvjf samtools-1.11.tar.bz2 && cd samtools-1.11/ && ./configure --prefix=/varpipe_wgs/tools/a/samtools && make && make install &&\
    cp /varpipe_wgs/tools/a/samtools/bin/samtools /varpipe_wgs/tools/ && cd / && rm -rf /build

RUN ln -s /usr/bin/python2.7 /usr/bin/python && ln -s /usr/bin/python2.7 /usr/bin/python2 &&\
    wget -O- https://bootstrap.pypa.io/pip/2.7/get-pip.py >get-pip.py && python get-pip.py &&\
    pip2 install pyyaml fpdf

RUN cd /varpipe_wgs/tools && wget -qO- https://get.nextflow.io | bash && chmod +x nextflow

ENV PATH=$PATH:/varpipe_wgs/tools:/varpipe_wgs/tools/htslib/bin:/varpipe_wgs/tools/samtools/bin

RUN cp -R /clockwork/nextflow /varpipe_wgs/tools/clockwork-0.11.3

WORKDIR /varpipe_wgs/data

ENV JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64

CMD /bin/bash