Dockerfile

# Create Flywheel Gear that can run dtiInit
# For source code see:
#   https://github.com/vistalab/vistasoft/raw/97aa8a8/mrDiffusion/dtiInit/standalone
#

# FROM ubuntu:trusty
FROM flywheel/matlab-mcr:v82
MAINTAINER Michael Perry <lmperry@stanford.edu>

# Install dependencies
RUN apt-get -qq update && apt-get -qq install -y \
    unzip \
    xorg \
    wget \
    curl \
    zip \
    gzip \
    python

# ADD the dtiInit Matlab Stand-Alone (MSA) into the container.
ADD https://github.com/vistalab/vistasoft/raw/97aa8a8/mrDiffusion/dtiInit/standalone/executables/dtiInit_glnxa64_v82 /usr/local/bin/dtiInit

# Add bet2 (FSL) to the container
ADD https://github.com/vistalab/vistasoft/raw/97aa8a8/mrAnatomy/Segment/bet2 /usr/local/bin/

# Add the MNI_EPI template and JSON schema files to the container
ADD https://github.com/vistalab/vistasoft/raw/97aa8a8/mrDiffusion/templates/MNI_EPI.nii.gz /templates/
ADD https://github.com/vistalab/vistasoft/raw/97aa8a8/mrDiffusion/dtiInit/standalone/dtiInitStandAloneJsonSchema.json /templates/

# Copy the help text to display when no args are passed in.
COPY source/doc/help.txt /opt/help.txt

# Ensure that the executable files are executable
RUN chmod +x /usr/local/bin/bet2 && chmod +x /usr/local/bin/dtiInit

# Configure environment variables for bet2
ENV FSLOUTPUTTYPE NIFTI_GZ

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

# Copy and configure code
COPY source/bin/run \
    source/bin/parse_config.py \
    manifest.json \
    ${FLYWHEEL}/
RUN chmod +x \
    ${FLYWHEEL}/run \
    ${FLYWHEEL}/parse_config.py

# Configure entrypoint
ENTRYPOINT ["/flywheel/v0/run"]