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author dcouvin
date Mon, 10 Jan 2022 20:06:07 +0000
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-1:000000000000 0:55051a9bc58d
1 FROM debian:stretch
2
3 ENV DEBIAN_FRONTEND noninteractive
4
5 ### RUN set -ex; \
6
7 RUN apt-get update -qq; \
8 apt-get install -y -qq git \
9 apt-utils \
10 wget \
11 python3-pip \
12 ncbi-blast+ \
13 libz-dev \
14 ; \
15 rm -rf /var/cache/apt/* /var/lib/apt/lists/*;
16
17 ENV DEBIAN_FRONTEND Teletype
18
19 # Install python dependencies
20 RUN pip3 install -U biopython==1.73 tabulate cgecore gitpython python-dateutil;
21
22 # RESFINDER setup
23 COPY run_resfinder.py /usr/src/run_resfinder.py
24
25 ADD cge /usr/src/cge
26 ADD tests /usr/src/tests
27
28 # Install kma
29 RUN cd /usr/src/cge; \
30 git clone --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \
31 cd kma && make; \
32 mv kma* /bin/
33
34
35 RUN chmod 755 /usr/src/run_resfinder.py
36 RUN chmod 755 /usr/src/tests/functional_tests.py
37
38
39 ENV PATH $PATH:/usr/src
40 # Setup .bashrc file for convenience during debugging
41 RUN echo "alias ls='ls -h --color=tty'\n"\
42 "alias ll='ls -lrt'\n"\
43 "alias l='less'\n"\
44 "alias du='du -hP --max-depth=1'\n"\
45 "alias cwd='readlink -f .'\n"\
46 "PATH=$PATH\n">> ~/.bashrc
47
48
49 # Change working directory
50 WORKDIR "/usr/src/"
51
52 # Execute program when running the container
53 ENTRYPOINT ["python3", "/usr/src/run_resfinder.py"]