Dockerfile

FROM continuumio/miniconda

RUN apt update
RUN apt install -y git build-essential

RUN conda config --add channels defaults --add channels bioconda --add channels conda-forge
RUN conda create -n raseenv prophyle ete3 pysam snakemake-minimal samtools parallel r-optparse pandas seqtk

RUN echo "source activate raseenv" > ~/.bashrc
RUN [ "/bin/bash", "-c", "source activate raseenv && pip install --upgrade git+git://github.com/prophyle/prophyle.git@b55e026" ]

WORKDIR /root
ADD https://github.com/c2-d2/rase-db-spneumoniae-sparc/releases/download/v1.3/spneumoniae-sparc.k18.tar.gz /root/database/

RUN [ "bash", "-c", "sed -i 's/\\(\\$(CC).*$\\)/\\1 $(LDFLAGS)/' /opt/conda/envs/raseenv/lib/python3.7/site-packages/prophyle/{*,*/*}/Makefile;\
sed -i 's/\\(\\$(CXX).*$\\)/\\1 $(LDFLAGS)/' /opt/conda/envs/raseenv/lib/python3.7/site-packages/prophyle/{*,*/*}/Makefile;\
sed -i 's/CFLAGS=/CFLAGS+=/' /opt/conda/envs/raseenv/lib/python3.7/site-packages/prophyle/prophyle_index/{,bwa/}Makefile;\
sed -i 's/CXXFLAGS  =/CXXFLAGS +=/' /opt/conda/envs/raseenv/lib/python3.7/site-packages/prophyle/prophyle_as*/Makefile" ]


RUN [ "/bin/bash", "-c", "source activate raseenv && prophyle decompress /root/database/spneumoniae-sparc.k18.tar.gz /root/database" ]