Dockerfile

FROM continuumio/miniconda
MAINTAINER Andreas Wilm <wilma@gis.a-star.edu.sg>
LABEL maintainer="wilma@gis.a-star.edu.sg" \
      description="Container image containing all requirements for the rpd-sg10k-grch38-gatk4gvcf pipeline"
ENV PATH /opt/conda/envs/rpd-sg10k-grch38-gatk4gvcf/bin:$PATH
COPY environment.yml /

# copied from https://github.com/nf-core/tools/blob/master/Dockerfile
# so that we can start from miniconda rather than nfcore/base
# Install procps so that Nextflow can poll CPU usage
# Also install gnuplot which seems broken in bio/conda at the
# time of writing due to missing libs 
RUN apt-get update && apt-get install -y procps gnuplot && apt-get clean -y
# Update the base version of conda
RUN /opt/conda/bin/conda update -n base conda

# nscc
RUN mkdir /data /seq

# sg10k-cov
RUN apt-get install -y build-essential zlib1g-dev libbz2-dev && \
    git clone https://andreas-wilm@bitbucket.org/andreas-wilm/sg10k-cov.git && \
    cd sg10k-cov/ && \
    git checkout 6b74ab8 && \
    bash make.sh && \
    cp sg10k-cov-062017.sh samtools-M /usr/local/bin/ && \
    cd .. && rm -rf sg10k-cov/ && \
    apt-get remove -y build-essential zlib1g-dev libbz2-dev && apt-get clean -y

RUN /opt/conda/bin/conda env create -f /environment.yml
RUN /opt/conda/bin/conda clean -a

CMD ["/bin/bash"]