Dockerfile

FROM python:3.8-slim-buster
ENV AWS_KEY=
ENV AWS_SEC_KEY=

WORKDIR /brainlit_dir

RUN apt-get update && apt-get install -y gcc libgl1-mesa-glx libxrender1
RUN apt install -y wget bzip2 vim

# install ilastik
RUN wget https://files.ilastik.org/ilastik-1.4.0-Linux.tar.bz2
RUN tar xjf ilastik-1.4.0-Linux.tar.bz2

# install brainlit
COPY . .
RUN pip install -e .


RUN chmod +x ./.aws.sh
RUN ./.aws.sh

CMD python experiments/BrainLine/scripts/soma_detect_image.py

# Old version
# FROM python:3.8-slim
# #RUN pip install --no-cache-dir matplotlib pandas numpy

# WORKDIR /usr/src/app

# #RUN apt-get update \
# #    && apt-get install -y --no-install-recommends git 
# #    && apt-get purge -y --auto-remove \
# RUN apt-get update
# RUN apt-get install -y --no-install-recommends \
#     make automake gcc g++ subversion python3-dev \
#     && rm -rf /var/lib/apt/lists/*


# # RUN apk add --no-cache --update \
# #     python3 python3-dev gcc \
# #     gfortran musl-dev

# # RUN apk update && apk upgrade && \
# #     apk add --no-cache bash git openssh

# # RUN git clone https://github.com/neurodata/brainlit.git

# RUN pip install --upgrade pip setuptools && \
#     pip install --no-cache-dir brainlit


# # create credentials file for aws
# # RUN chmod +x .aws.sh && \ 
# #     source .aws.sh