Dockerfile.devel

#########################################
# SciF Base
#
# docker build -f Dockerfile.devel -t vanessa/cseq-dev .
# docker run vanessa/cseq-dev
#
#########################################

FROM continuumio/miniconda3

#########################################
# SciF Install

ADD . /
RUN apt-get update && apt-get install -y git wget build-essential \
                                         gcc-multilib apt-utils \
                                         zlib1g-dev samtools 

RUN /opt/conda/bin/conda install -y numpy scipy &&  \
    /opt/conda/bin/pip install biopython

RUN git clone https://github.com/lh3/seqtk.git build && \
            cd build && git checkout v1.2 && make && mv seqtk /usr/local/bin

RUN /opt/conda/bin/pip install scif
RUN chmod u+x /entrypoint.sh

# Install the filesystem from the recipe
RUN scif install /carrierseq-dev.scif

# Labels
LABEL bioRxiv-doi https://doi.org/10.1101/175281

# SciF Entrypoint

ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]