Dockerfile_devel

FROM nipreps/fmriprep:unstable

# net-tools needed for code-server
# wget necessary for data downloads
RUN apt-get update &&\
    apt-get install -y \
        net-tools \
        wget

# necessary to find fmriprep in /src/fmriprep
ENV PYTHONNOUSERSITE=0

RUN cd /src/fmriprep &&\
    pip install --no-use-pep517 -e .[all] &&\
    cp -R /src/fmriprep/fmriprep.egg-info /src/

# create freesurfer license
RUN cd /tmp &&\
    echo 'cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==' | base64 -d | sh

ENV FS_LICENSE=/tmp/license.txt

# set the fmriprep development variables
ENV FMRIPREP_REGRESSION_SOURCE=/tmp/data/fmriprep_bold_truncated \
    FMRIPREP_REGRESSION_TARGETS=/tmp/data/fmriprep_bold_mask \
    FMRIPREP_REGRESSION_REPORTS=/tmp/data/reports \
    FMRIPREP_DEV=1

# use flake8 as linter
RUN conda install -y flake8

RUN mkdir -p /tmp/data

# Download ds005
RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
         -O ds005_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32a429ad5a101f977eb75" &&\
    tar xvzf ds005_downsampled.tar.gz -C /tmp/data/ &&\
    rm ds005_downsampled.tar.gz

# Download ds210
RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
         -O ds210_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/5ae9e37b9a64d7000ce66c21" &&\
    tar xvzf ds210_downsampled.tar.gz -C /tmp/data &&\
    rm ds210_downsampled.tar.gz

# Download ds054
RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
         -O ds054_downsampled.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/57f32c22594d9001ef91bf9e" &&\
    tar xvzf ds054_downsampled.tar.gz -C /tmp/data &&\
    rm ds054_downsampled.tar.gz

# Download freesurfer results for ds005
RUN mkdir -p /tmp/ds005/derivatives &&\
    wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
         -O ds005_derivatives_freesurfer.tar.gz "https://files.osf.io/v1/resources/fvuh8/providers/osfstorage/58fe59eb594d900250960180" &&\
   tar xvzf ds005_derivatives_freesurfer.tar.gz -C /tmp/ds005/derivatives &&\
   rm ds005_derivatives_freesurfer.tar.gz

# Download truncated bold images
RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
         -O fmriprep_bold_truncated.tar.gz "https://osf.io/286yr/download" &&\
    tar xvzf fmriprep_bold_truncated.tar.gz -C /tmp/data &&\
    rm fmriprep_bold_truncated.tar.gz

# Download precomputed masks
RUN wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q \
         -O fmriprep_bold_mask.tar.gz "https://osf.io/s4f7b/download" &&\
    tar xvzf fmriprep_bold_mask.tar.gz -C /tmp/data &&\
    rm fmriprep_bold_mask.tar.gz

# set up code-server (need net-tools for initialization) - V2.1665-vsc1.39.2
RUN curl -o /tmp/code-server.tar.gz -SL https://github.com/cdr/code-server/releases/download/2.1665-vsc1.39.2/code-server2.1665-vsc1.39.2-linux-x86_64.tar.gz

RUN mkdir /src/codeserver &&\
    tar -xvf /tmp/code-server.tar.gz -C /src/codeserver --strip-components=1

RUN /src/codeserver/code-server --install-extension eamodio.gitlens &&\
    /src/codeserver/code-server --install-extension ms-python.python
    

ENTRYPOINT ["/src/codeserver/code-server", "--auth", "none", "/src/fmriprep"]

# usage example (assuming in local fmriprep directory):
#
# docker run -it \
# -p 127.0.0.1:8445:8080 \
# -v ${PWD}:/src/fmriprep \
# fmriprep_devel:latest
#
# then type 127.0.0.1:8445 in your browser address bar