Dockerfile.gpu

FROM continuumio/conda-ci-linux-64-python3.8:latest as base

ARG BRAINY_COMMITISH="19e69299"

USER root

RUN apt-get update \
    && apt-get install --yes --quiet --no-install-recommends \
        ca-certificates \
        git \
        libgomp1 \
    && rm -rf /var/lib/apt/lists/*

RUN conda install -c conda-forge --yes git-annex && conda clean --all

RUN pip install --quiet --no-cache-dir datalad datalad-osf

WORKDIR /opt/neuronets/trained-models
ENV BRAINY_MODEL_FILE="/opt/neuronets/trained-models/neuronets/brainy/0.1.0/brain-extraction-unet-128iso-model.h5"

RUN datalad clone https://github.com/neuronets/trained-models.git . \
    && git config user.name "brainy" \ 
    && git config user.email "brainy" \   
    && datalad get -s osf-storage "$BRAINY_MODEL_FILE" \
    && git checkout "$BRAINY_COMMITISH"


FROM tensorflow/tensorflow:2.3.1-gpu
ARG DEBIAN_FRONTEND="noninteractive"

COPY --from=base /opt/neuronets/trained-models /opt/neuronets/trained-models

ENV LANG="C.UTF-8" \
    LC_ALL="C.UTF-8"

RUN apt-get update \
    && apt-get install --yes --quiet --no-install-recommends \
        ca-certificates \
        git \
        libgomp1 \
    && rm -rf /var/lib/apt/lists/*

WORKDIR /opt/neuronets/brainy
COPY . .

ENV BRAINY_MODEL_FILE="/opt/neuronets/trained-models/neuronets/brainy/0.1.0/brain-extraction-unet-128iso-model.h5"

# Only difference between this and cpu Dockerfile is this line.
RUN pip install --no-cache-dir --editable .

ENV FREESURFER_HOME="/opt/neuronets/brainy/freesurfer"
ENV PATH="$FREESURFER_HOME/bin:$PATH"

WORKDIR /data
ENTRYPOINT ["brainy"]
LABEL maintainer="Hoda Rajaei <rajaei.hoda@gmail.com>"