Mercurial > repos > dcouvin > resfinder4
comparison resfinder/dockerfile @ 0:55051a9bc58d draft default tip
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author | dcouvin |
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date | Mon, 10 Jan 2022 20:06:07 +0000 |
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-1:000000000000 | 0:55051a9bc58d |
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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"] |