Dockerfile

FROM continuumio/miniconda3

ENV LC_ALL en_US.UTF-8



WORKDIR /app

# Make RUN commands use `bash --login`:
SHELL ["/bin/bash", "--login", "-c"]


# Create the environment:
RUN git clone https://github.com/kblin/covid-spike-classification.git covid-spike-classification


RUN cd covid-spike-classification && HASH_COMMIT=$(git rev-parse HEAD) && echo $HASH_COMMIT && cd ..
LABEL HASH_COMMIT=$HASH_COMMIT


RUN cd covid-spike-classification/ && git log | head && cd ..

RUN conda env create -n csc -f covid-spike-classification/environment.yml
RUN conda activate csc
RUN cd covid-spike-classification && pip install covid-spike-classification && cd ..


# Initialize conda in bash config files:
RUN conda init bash

# Activate the environment, and make sure it's activated:
RUN echo "conda activate csc" > ~/.bashrc


# Add the csc conda bin-dir
ENV PATH /opt/conda/envs/csc/bin:$PATH