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author dcouvin
date Mon, 06 Sep 2021 16:00:46 +0000
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-1:000000000000 0:140d4f9e1f20
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==1.3.2;
21
22 # Install kma
23 RUN git clone --branch 1.0.1 --depth 1 https://bitbucket.org/genomicepidemiology/kma.git; \
24 cd kma && make; \
25 mv kma* /bin/
26
27 COPY pmlst.py /usr/src/pmlst.py
28
29 RUN chmod 755 /usr/src/pmlst.py;
30
31 ENV PATH $PATH:/usr/src
32 # Setup .bashrc file for convenience during debugging
33 RUN echo "alias ls='ls -h --color=tty'\n"\
34 "alias ll='ls -lrt'\n"\
35 "alias l='less'\n"\
36 "alias du='du -hP --max-depth=1'\n"\
37 "alias cwd='readlink -f .'\n"\
38 "PATH=$PATH\n">> ~/.bashrc
39
40 WORKDIR /workdir
41
42 # Execute program when running the container
43 ENTRYPOINT ["/usr/src/pmlst.py"]