Dockerfile

FROM python:3.7

# Setup paths:
ENV DIRPATH /sbc_ngs
WORKDIR $DIRPATH
COPY . .
ENV PYTHONPATH="$DIRPATH:$PYTHONPATH"

# Setup ARG variables:
ARG BWA_BIN="bwa-0.7.17.tar.bz2"
ARG BWA_VERSION="0.7.17"
ARG SAMTOOLS_BIN="samtools-1.6.tar.bz2"
ARG SAMTOOLS_VERSION="1.6"
ARG BCFTOOLS_BIN="bcftools-1.6.tar.bz2"
ARG BCFTOOLS_VERSION="1.6"

# Install libraries:
RUN apt-get update && apt-get install -y --no-install-recommends \
	build-essential \
	ca-certificates \
	curl \
	libbz2-dev \
	liblzma-dev \
	libncurses5-dev \
	libncursesw5-dev \
	zlib1g-dev \
	&& rm -rf /var/lib/apt/lists/*

# Download and install bwa:
RUN curl -fsSL https://github.com/lh3/bwa/releases/download/v$BWA_VERSION/$BWA_BIN -o /opt/$BWA_BIN \
	&& tar xjf /opt/$BWA_BIN -C /opt/ \
	&& cd /opt/bwa-$BWA_VERSION \
	&& pwd \
	&& ls -l \
	&& make \
	&& mv bwa /usr/local/bin/ \
	&& rm /opt/$BWA_BIN

# Download and install samtools:
RUN curl -fsSL https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/$SAMTOOLS_BIN -o /opt/$SAMTOOLS_BIN \
	&& tar xjf /opt/$SAMTOOLS_BIN -C /opt/ \
	&& cd /opt/samtools-$SAMTOOLS_VERSION \
	&& make \
	&& make install \
	&& rm /opt/$SAMTOOLS_BIN

# Download and install bcftools:
RUN curl -fsSL https://github.com/samtools/bcftools/releases/download/$BCFTOOLS_VERSION/$BCFTOOLS_BIN -o /opt/$BCFTOOLS_BIN \
	&& tar xjf /opt/$BCFTOOLS_BIN -C /opt/ \
	&& cd /opt/bcftools-$BCFTOOLS_VERSION \
	&& make \
	&& make install \
	&& rm /opt/$BCFTOOLS_BIN

# Install Python dependencies:
RUN pip install --upgrade pip \
  && pip install -r requirements.txt
  
# Set ENTRYPOINT:
ENTRYPOINT ["python", "-u", "app.py"]