FROM snakemake/snakemake:stable
ADD cloudbatch-snakemake-highmem.sh .
ADD cloudbatch-snakemake-highcpu.sh .
ADD env.yaml .

RUN /bin/bash -c "chmod 755 /tmp/repo/cloudbatch-snakemake-high*.sh"

#installation of the mapping environment
RUN /bin/bash -c "mamba env create -f env.yaml"
RUN echo "source activate mapping" > ~/.bashrc

#RUN curl -sSL https://sdk.cloud.google.com | bash
RUN apt-get update && \
    apt-get install -y curl gnupg && \
    echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
    curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg  add - && \
    apt-get update -y && \
    apt-get install google-cloud-sdk -y
