lettersim-ot-rsa/Dockerfile

FROM continuumio/miniconda3:24.7.1-0
WORKDIR /analysis

COPY . .

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

# install git & git-annex
RUN apt-get install -y curl

# download the dataset with git (files will be tracked with git-annex)
# https://openneuro.org/datasets/ds005594
# (alternatively, comment this line out and place the data in the docker directory before building, as a directory named 'eeg')
# RUN git clone https://github.com/OpenNeuroDatasets/ds005594 eeg
# RUN git -C eeg annex get --all
# RUN datalad install https://github.com/OpenNeuroDatasets/ds005594.git eeg
RUN (cd eeg && ./download_raw_eeg.sh)

# install TexLive 2023 (used in some figures)
# see https://www.tug.org/historic/ for other mirrors
RUN wget ftp://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2023/install-tl-unx.tar.gz
RUN zcat < install-tl-unx.tar.gz | tar xf -
RUN perl install-tl-2023*/install-tl --no-interaction --scheme=basic --repository=ftp://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2023/tlnet-final/
ENV PATH="/usr/local/texlive/2023/bin/x86_64-linux:$PATH"
RUN rm -r install-tl-*

# install TexLive packages
RUN tlmgr init-usertree
RUN tlmgr install xcolor tex-gyre underscore etoolbox pgf

# install environments for Python and R
RUN conda env create -f env/environment-mne.yml
RUN conda env create -f env/environment-rdms.yml
RUN conda env create -f env/environment-r.yml

# set up fonts for matplotlib
RUN conda run -n mne --no-capture-output python fig_code/mpl_setup_fonts.py
RUN conda run -n rdms --no-capture-output python fig_code/mpl_setup_fonts.py

# unbuffered stdout & stderr streams by default
ENV PYTHONUNBUFFERED=1

# disable healthchecks, to address containers dying with code Exited(137) bug when OOMKilled=False
HEALTHCHECK NONE