|
0
|
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"] |
