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Dockerfile
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# Use an official Python runtime as a parent image
FROM python:3.10.6-slim
ARG TAG
# 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 python3-openssl git tabix \
freebayes && \
apt-get clean
# Install gsort
RUN \
cd /usr/local/bin && \
curl -s https://api.github.com/repos/brentp/gsort/releases/latest \
| grep browser_download_url \
| grep -i $(uname) \
| cut -d '"' -f 4 \
| wget -O gsort -qi - && \
chmod +x gsort
RUN pip install pandas xlsxwriter pyfastx scipy pysam pyyaml
RUN pip install mitywgs==${TAG}
WORKDIR /home
ENTRYPOINT [ "mity" ]