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FROM python:3.10-slim-bullseye
ENV INSIDE_DOCKER true
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update -qq; \
apt-get install --no-install-recommends -y -qq git \
build-essential \
wget \
ncbi-blast+ \
libz-dev \
procps \
; \
rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
# Install KMA
RUN cd /usr/src/; \
git clone --depth 1 -b 1.4.11 https://bitbucket.org/genomicepidemiology/kma.git; \
cd kma && make; \
mv kma /usr/bin/; \
cd ..; \
rm -rf kma/;
ENV RESFINDER_VERSION 4.4.2
# Install ResFinder
RUN pip install --no-cache-dir resfinder==$RESFINDER_VERSION
# Install databases
RUN cd /; \
mkdir databases; \
cd /databases/; \
git clone -b resfinder-$RESFINDER_VERSION --depth 1 https://git@bitbucket.org/genomicepidemiology/resfinder_db.git; \
git clone -b resfinder-$RESFINDER_VERSION --depth 1 https://git@bitbucket.org/genomicepidemiology/pointfinder_db.git; \
git clone -b resfinder-$RESFINDER_VERSION --depth 1 https://git@bitbucket.org/genomicepidemiology/disinfinder_db.git; \
cd /databases/resfinder_db; \
python INSTALL.py; \
rm -rf .git; \
cd /databases/pointfinder_db; \
python INSTALL.py; \
rm -rf .git; \
cd /databases/disinfinder_db; \
python INSTALL.py; \
rm -rf .git;
# Setup environment
RUN cd /; \
mkdir app;
WORKDIR /app
# Environmental variables
ENV CGE_RESFINDER_RESGENE_DB /databases/resfinder_db/
ENV CGE_RESFINDER_RESPOINT_DB /databases/pointfinder_db/
ENV CGE_DISINFINDER_DB /databases/disinfinder_db/
# Execute program when running the container
ENTRYPOINT ["python", "-m", "resfinder"]
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