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Dockerfile
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# Use an official Python runtime as a parent image
FROM python:3.7.4-slim
# Install freebayes dependencies
RUN apt-get update -yqq && \
apt-get install -yqq \
make build-essential libssl-dev zlib1g-dev libbz2-dev \
libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev \
xz-utils tk-dev libffi-dev liblzma-dev python-openssl git tabix && \
apt-get clean
# Install freebayes
RUN \
# Clone and compile freebayes
git config --global url.https://github.com/.insteadOf git://github.com/ && \
cd /opt && \
git clone --recursive --branch v1.2.0 git://github.com/ekg/freebayes.git && \
cd freebayes && \
make && \
make install && \
\
# Install htslib
cd /tmp && \
wget "https://github.com/samtools/htslib/releases/download/1.8/htslib-1.8.tar.bz2" && \
tar -vxjf htslib-1.8.tar.bz2 && \
cd htslib-1.8 && \
./configure --disable-bz2 --disable-lzma && \
make && \
make install && \
rm -rf /tmp/htslib-1.8 && \
\
# Install bcftools
cd /tmp && \
wget "https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2" && \
tar -vxjf bcftools-1.9.tar.bz2 && \
cd bcftools-1.9 && \
./configure --disable-bz2 --disable-lzma && \
make && \
make install && \
rm -rf /tmp/bcftools-1.9
ENV PATH $PATH:/opt/freebayes/scripts/:/opt/freebayes/vcflib/scripts/:/opt
# Install gsort
RUN \
cd /usr/local/bin && \
curl -s https://api.github.com/repos/brentp/gsort/releases/latest \
| grep browser_download_url \
| grep -i $(uname) \
| cut -d '"' -f 4 \
| wget -O gsort -qi - && \
chmod +x gsort
# Install mity from dev server (but first install the previous version to get the dependencies from pypi)
#RUN pip install mitywgs==0.2.2
#RUN pip install -i https://test.pypi.org/simple/ mitywgs==0.2.2rc2
# Install mity
RUN pip install mitywgs==0.3.0
WORKDIR /home
ENTRYPOINT [ "mity" ]