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Dockerfile
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Dockerfile
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FROM imperialgenomicsfacility/base-notebook-image:release-v0.0.7.1
LABEL maintainer="imperialgenomicsfacility"
LABEL version="0.0.1"
LABEL description="Docker image for running RNA-Seq analysis"
ENV NB_USER vmuser
ENV NB_UID 1000
USER root
WORKDIR /
RUN apt-get -y update && \
apt-get install --no-install-recommends -y \
libfontconfig1 \
libxrender1 \
libreadline-dev \
libreadline7 \
libicu-dev \
libc6-dev \
icu-devtools \
libjpeg-dev \
libxext-dev \
libcairo2 \
libicu60 \
libicu-dev \
gcc \
g++ \
make \
libgcc-5-dev \
gfortran \
libncurses5-dev \
libbz2-1.0 \
libbz2-dev \
liblzma5 \
liblzma-dev \
curl \
git && \
apt-get purge -y --auto-remove && \
apt-get clean && \
rm -rf /var/lib/apt/lists/* && \
npm install --global http-server
USER $NB_USER
WORKDIR /home/$NB_USER
ENV TMPDIR=/home/$NB_USER/.tmp
ENV PATH=$PATH:/home/$NB_USER/miniconda3/bin/
RUN rm -f /home/$NB_USER/environment.yml && \
rm -f /home/$NB_USER/Dockerfile
COPY environment.yml /home/$NB_USER/environment.yml
COPY Dockerfile /home/$NB_USER/Dockerfile
COPY examples /home/$NB_USER/examples
USER root
RUN chown ${NB_UID} /home/$NB_USER/environment.yml && \
chown ${NB_UID} /home/$NB_USER/Dockerfile && \
chown -R ${NB_UID} /home/$NB_USER/examples
USER $NB_USER
WORKDIR /home/$NB_USER
RUN . /home/$NB_USER/miniconda3/etc/profile.d/conda.sh && \
conda update -n base -c defaults conda && \
conda env update -q -n notebook-env --file /home/$NB_USER/environment.yml && \
jupyter serverextension enable --sys-prefix jupyter_server_proxy && \
jupyter labextension install dask-labextension && \
jupyter labextension install @jupyter-widgets/jupyterlab-manager && \
jupyter labextension install @bokeh/jupyter_bokeh && \
conda clean -a -y && \
rm -rf /home/$NB_USER/.cache && \
rm -rf /tmp/* && \
rm -rf ${TMPDIR} && \
mkdir -p ${TMPDIR} && \
mkdir -p /home/$NB_USER/.cache && \
find miniconda3/ -type f -name *.pyc -exec rm -f {} \;
RUN mkdir -p /home/$NB_USER/bin && \
wget -q -O /home/$NB_USER/bin/fastp http://opengene.org/fastp/fastp && \
chmod a+x /home/$NB_USER/bin/fastp && \
wget -q -O /tmp/samtools-1.10.tar.bz2 https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 && \
cd /tmp && \
tar -jxf /tmp/samtools-1.10.tar.bz2 && \
cd samtools-1.10/ && \
./configure --prefix=/home/vmuser/bin/samtools && \
make && \
make install && \
cd /home/$NB_USER/ && \
rm -rf /tmp/samtools-1.10 && \
wget -q -O /tmp/fastqc_v0.11.9.zip https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip && \
cd /tmp && \
unzip fastqc_v0.11.9.zip && \
mv /tmp/FastQC /home/$NB_USER/bin && \
chmod a+x /home/$NB_USER/bin/FastQC/fastqc && \
cd /home/$NB_USER/ && \
rm -rf /tmp/fastqc_v0.11.9.zip && \
wget -q -O /tmp/2.7.3a.tar.gz https://github.com/alexdobin/STAR/archive/2.7.3a.tar.gz && \
cd /tmp && \
tar -xzf 2.7.3a.tar.gz && \
mv STAR-2.7.3a /home/$NB_USER/bin && \
cd /home/$NB_USER/ && \
rm -rf /tmp/2.7.3a.tar.gz && \
wget -q -O /tmp/0.6.5.tar.gz https://github.com/FelixKrueger/TrimGalore/archive/0.6.5.tar.gz && \
cd /tmp && \
tar -xzf 0.6.5.tar.gz && \
mv TrimGalore-0.6.5 /home/$NB_USER/bin && \
cd /home/$NB_USER/ && \
rm -rf /tmp/0.6.5.tar.gz
ENV LC_ALL C.UTF-8
ENV LANG C.UTF-8
ENV PATH /home/$NB_USER/bin:${PATH}
ENV PATH /home/$NB_USER/bin/samtools/bin/:${PATH}
ENV PATH /home/$NB_USER/bin/FastQC/:${PATH}
ENV PATH /home/$NB_USER/bin/STAR-2.7.3a/bin/Linux_x86_64_static/:${PATH}
ENV PATH /home/$NB_USER/bin/TrimGalore-0.6.5:${PATH}
EXPOSE 8888
EXPOSE 8080
CMD [ "notebook" ]