Dockerfile

# scitran/dcm-convert
#
# Use SciTran Data lib to convert raw DICOM data (zip) from Siemens or GE to
# various formats (montage, nifti, png).
# See https://github.com/scitran/data for source code.
#

FROM ubuntu-debootstrap:trusty

MAINTAINER Michael Perry <lmperry@stanford.edu>

# Install dependencies
RUN apt-get update && apt-get -y install python-dev \
   python-virtualenv \
   git \
   libjpeg-dev \
   zlib1g-dev

# Link libs: pillow jpegi and zlib support hack
RUN ln -s /usr/lib/x86_64-linux-gnu/libjpeg.so /usr/lib
RUN ln -s /usr/lib/x86_64-linux-gnu/libz.so /usr/lib

# Install scitran.data dependencies
RUN pip install \
    numpy==1.9.0 \
    pytz \
    pillow \
    git+https://github.com/scitran/pydicom.git@0.9.9_value_vr_mismatch \
    git+https://github.com/nipy/nibabel.git@3bc31e9a6191fc54667b3387ed5dfaced46bf755 \
    git+https://github.com/moloney/dcmstack.git@6d49fe01235c08ae63c76fa2f3943b49c9b9832d \
    git+https://github.com/scitran/data.git@bad266cbf7d284738bb8f426c7ca8ecc9de50bb5

# Make directory for flywheel spec (v0)
ENV FLYWHEEL /flywheel/v0
RUN mkdir -p ${FLYWHEEL}

# Put the code in place
COPY run \
    manifest.json \
    dcm-convert.py \
    ${FLYWHEEL}/

# Set the entrypoint
ENTRYPOINT ["/flywheel/v0/run"]