Container that encapsulates the classifier and pre-processing steps

[skwarfield]

It would be convenient to have a container, such as a docker container, that includes all of the software and data needed to apply the MELD classifier to a subject.

An example of a Dockerfile that would build such an environment is here:

FROM ubuntu:jammy AS FCDDetection
ENV DEBIAN_FRONTEND="noninteractive"

Update the ubuntu.

RUN apt-get -y update &&
apt-get -y upgrade

Install the prerequisite software

RUN apt-get install -y build-essential
apt-utils
vim
nano
curl
wget
pip
python3
git

Install freesurfer in /opt/freesurfer.

RUN mkdir -p /freesurfertar
&& curl -SL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz
| tar -xzC /freesurfertar
&& mv /freesurfertar/freesurfer /opt/
&& rmdir /freesurfertar

This will also need to be configured in the running docker container.

This modifies only the build environment.

ENV PATH=/opt/freesurfer/bin:$PATH
RUN echo "PATH=/opt/freesurfer/bin:$PATH" >> ~/.bashrc
ENV FREESURFER_HOME=/opt/freesurfer
RUN echo "FREESURFER_HOME=/opt/freesurfer" >> ~/.bashrc

Install miniconda

ENV CONDA_DIR /opt/conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh &&
/bin/bash ~/miniconda.sh -b -p /opt/conda

Put conda in path so we can use conda activate

ENV PATH=$CONDA_DIR/bin:$PATH

Update to the newest version of conda:

RUN conda update -n base -c defaults conda

RUN conda init bash

checkout and install the github repo

RUN cd / && git clone https://github.com/MELDProject/meld_classifier.git

enter the meld_classifier directory

create the meld classifier environment with all the dependencies

SHELL ["/bin/bash", "-c"]
RUN cd /meld_classifier && conda env create -f environment.yml
RUN cd /meld_classifier && conda run -n meld_classifier /bin/bash -c "pip install -e ."

Use the bash shell this way because conda cant activate.

#SHELL ["conda", "run", "-n", "meld_classifier", "/bin/bash", "-c"]

Configure MELD for this docker image:

COPY ./meld_config.ini /meld_classifier/meld_config.ini
RUN mkdir /MELD-data

RUN conda run --no-capture-output -n meld_classifier /bin/bash -c " python3 /meld_classifier/scripts/prepare_classifier.py --skip-config"

COPY user-freesurfer-license.txt ${FREESURFER_HOME}/.license

RUN cd /meld_classifier && conda run --no-capture-output -n meld_classifier /bin/bash -c " pytest "