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Dockerfile
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FROM imperialgenomicsfacility/base-notebook-image:release-v0.0.7
LABEL maintainer="imperialgenomicsfacility"
LABEL version="0.0.1"
LABEL description="Docker image for running pipeline tutorials"
ENV NB_USER vmuser
ENV NB_UID 1000
USER root
WORKDIR /
RUN apt-get -y update && \
apt-get install --no-install-recommends -y \
build-essential \
libseccomp-dev \
pkg-config \
squashfs-tools \
cryptsetup \
libfontconfig1 \
libxrender1 \
libreadline-dev \
libreadline7 \
libicu-dev \
libc6-dev \
icu-devtools \
libjpeg-dev \
libxext-dev \
libcairo2 \
libicu60 \
gcc \
g++ \
make \
libgcc-5-dev \
gfortran \
default-jre \
default-jdk-headless \
libssl-dev \
uuid-dev \
libgpgme11-dev \
git && \
apt-get purge -y --auto-remove && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
WORKDIR /tmp
RUN curl -s https://get.nextflow.io | bash \
&& mv nextflow /usr/local/bin/ \
&& chmod +x /usr/local/bin/nextflow \
&& chmod +r /usr/local/bin/nextflow \
&& rm -rf /tmp/nextflow* \
&& rm -rf /tmp/*
USER $NB_USER
WORKDIR /home/$NB_USER
ENV TMPDIR=/tmp
ENV PATH=$PATH:/home/$NB_USER/miniconda3/bin/
RUN rm -f /home/$NB_USER/environment.yml && \
rm -f /home/$NB_USER/Dockerfile
COPY environment.yaml /home/$NB_USER/environment.yaml
COPY Dockerfile /home/$NB_USER/Dockerfile
USER root
RUN chown ${NB_UID} /home/$NB_USER/environment.yaml && \
chown ${NB_UID} /home/$NB_USER/Dockerfile
USER $NB_USER
WORKDIR /home/$NB_USER
RUN conda env update -q -n notebook-env --file /home/$NB_USER/environment.yaml && \
conda clean -a -y && \
rm -rf /home/$NB_USER/.cache && \
rm -rf /tmp/* && \
mkdir -p /home/$NB_USER/.cache && \
find miniconda3/ -type f -name *.pyc -exec rm -f {} \;
EXPOSE 8888
EXPOSE 8080
CMD [ "notebook" ]