build_docker

# This is a Dockerfile, but we use a non-default name to prevent mybinder from
# using it. we also don't expect people to build the docker image themselves, so
# hopefully it shouldn't trip people up.

FROM mambaorg/micromamba

# git is necessary for one of the packages we install via pip, gcc is required
# to install another one of those packages, and we need to be root to use apt
USER root
RUN apt -y update
RUN apt -y install git gcc

# switch back to the default user
USER micromamba

# create the directory we'll put our dependencies in.
RUN mkdir -p /home/sfp_user/
# copy over the conda environment yml file
COPY ./environment.yml /home/sfp_user/sfp-environment.yml

# install the required python packages and remove unnecessary files.
RUN micromamba install -n base -y -f /home/sfp_user/sfp-environment.yml && \
    micromamba clean --all --yes

# get the specific commit of the MRI_tools repo that we need
RUN git clone https://github.com/WinawerLab/MRI_tools.git /home/sfp_user/MRI_tools; cd /home/sfp_user/MRI_tools; git checkout 8508652bd9e6b5d843d70be0910da413bbee432e
# get the matlab toolboxes that we need
RUN git clone https://github.com/cvnlab/GLMdenoise.git /home/sfp_user/GLMdenoise
RUN git clone https://github.com/vistalab/vistasoft.git /home/sfp_user/vistasoft
# get the slurm snakemake profile
RUN mkdir -p /home/sfp_user/.config/snakemake
RUN git clone -b singularity https://github.com/billbrod/snakemake-slurm.git /home/sfp_user/.config/snakemake/slurm

# copy over the env.sh file, which sets environmental variables
COPY ./singularity_env.sh /home/sfp_user/singularity_env.sh