Dockerfile

# Create Flywheel Gear that can run functional_preprocessing
# This pipeline is created by FSL and AFNI software, it is normally used to preprocess the fMRI data

# Start with the miykael/nipype_advanced Environment
FROM miykael/nipype_advanced
MAINTAINER Long Qian <longqianad@pku.edu.cn>

# Install dependencies
USER root

COPY ./sources.list /
RUN mv /etc/apt/sources.list /etc/apt/sources.list.bak
RUN mv /sources.list /etc/apt/
RUN mv /etc/apt/sources.list.d/neurodebian.sources.list /neurodebian.sources.list

RUN apt-get update \
    && apt-get install -y \
    zip \
    gzip \
    jq

# ADD the MNI template files into container

ADD https://github.com/mricenter/mri-templates/raw/master/1mm/ch2_1mm.nii /tmp/
ADD https://github.com/mricenter/mri-templates/raw/master/2mm/T1_bet_2mm.nii /tmp/
ADD https://github.com/mricenter/mri-templates/raw/master/3mm/T1_3mm.nii /tmp/



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


# Copy and configure run script and metadata code
COPY run ${FLYWHEEL}/run
RUN chmod +x ${FLYWHEEL}/run
COPY manifest.json ${FLYWHEEL}/manifest.json
ADD https://raw.githubusercontent.com/scitran/utilities/daf5ebc7dac6dde1941ca2a6588cb6033750e38c/metadata_from_gear_output.py ${FLYWHEEL}/metadata_create.py
RUN chmod +x ${FLYWHEEL}/metadata_create.py

RUN mv /neurodebian.sources.list /etc/apt/sources.list.d/neurodebian.sources.list
# Configure entrypoint
RUN rm /etc/apt/sources.list
RUN mv /etc/apt/sources.list.bak /etc/apt/sources.list
ENTRYPOINT ["/flywheel/v0/run"]