Dockerfile

FROM cggh/biipy_base:v1.1
MAINTAINER Nicholas Harding <njh@well.ox.ac.uk>

# Install APE via conda
RUN conda install --yes -c r --name science r-ape=3.3

# python modules via conda
ENV HDF5_DIR /usr/lib/x86_64-linux-gnu/hdf5/serial
ADD conda_package_list.txt .
RUN conda install --yes --name science --file conda_package_list.txt 
RUN conda install --yes --name science -c bpeng simupop=1.1.7

# install bwa, samtools & tabix from bioconda
RUN conda install --yes --name science bwa=0.7.13
RUN conda install --yes --name science samtools=1.3.1
RUN conda install --yes --name science htslib=1.3.1

# Add custom install scripts
RUN mkdir -p /etc/pki/tls/certs
RUN cp /etc/ssl/certs/ca-certificates.crt /etc/pki/tls/certs/ca-bundle.crt
RUN mkdir /biipy

# Install additional python libraries via pip. Versions not on conda.
# try to do some of these via conda-skeleton/build in future
ADD pypi_package_list.txt .
RUN source activate science && \
  pip install --no-cache-dir -r pypi_package_list.txt

ENV DISPLAY :0
ENV QT_X11_NO_MITSHM 1
EXPOSE 8888
ADD ./test.py /biipy/test.py
RUN source activate science && python3.5 /biipy/test.py
ADD ./test.ipynb /biipy/test.ipynb
ADD ./scripts /biipy/scripts
ADD ./version /biipy/version
RUN chmod -R 775 /biipy
CMD /biipy/scripts/notebook.sh