/
Dockerfile
101 lines (76 loc) · 3.29 KB
/
Dockerfile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
FROM ubuntu:14.04
RUN apt-get update && apt-get upgrade -y
RUN apt-get install -y git make g++ gcc \
python wget \
python-dev \
autoconf \
git \
curl \
python-pip \
libgsl0-dev \
zlib1g-dev \
libpq-dev \
libbluetooth-dev
ADD requirements.txt /tmp/requirements.txt
RUN pip install -r /tmp/requirements.txt
# Install Capnproto (mash dependency)
RUN curl https://capnproto.org/capnproto-c++-0.5.3.tar.gz --output capnproto-c++-0.5.3.tar.gz
RUN tar zxf capnproto-c++-0.5.3.tar.gz
RUN sh capnproto-c++-0.5.3/configure
RUN make -j6 check
RUN make install
RUN git clone https://github.com/marbl/Mash.git
RUN cd Mash \
&& sh bootstrap.sh \
&& ./configure \
&& make \
&& make install
# Add the PostgreSQL PGP key to verify their Debian packages.
# It should be the same key as https://www.postgresql.org/media/keys/ACCC4CF8.asc
RUN apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys B97B0AFCAA1A47F044F244A07FCC7D46ACCC4CF8
# Add PostgreSQL's repository. It contains the most recent stable release
# of PostgreSQL, ``9.3``.
RUN echo "deb http://apt.postgresql.org/pub/repos/apt/ precise-pgdg main" > /etc/apt/sources.list.d/pgdg.list
# Install ``python-software-properties``, ``software-properties-common`` and PostgreSQL 9.3
# There are some warnings (in red) that show up during the build. You can hide
# them by prefixing each apt-get statement with DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y python-software-properties software-properties-common postgresql-9.3 postgresql-client-9.3 postgresql-contrib-9.3
# Note: The official Debian and Ubuntu images automatically ``apt-get clean``
# after each ``apt-get``
RUN sudo usermod -aG sudo,adm postgres
RUN echo "root:docker" | chpasswd
RUN echo "postgres:docker" | chpasswd
# Run the rest of the commands as the ``postgres`` user created by the ``postgres-9.3`` package when it was ``apt-get installed``
USER postgres
# Create a PostgreSQL role named ``docker`` with ``docker`` as the password and
# then create a database `docker` owned by the ``docker`` role.
# Note: here we use ``&&\`` to run commands one after the other - the ``\``
# allows the RUN command to span multiple lines.
RUN /etc/init.d/postgresql start &&\
psql --command "CREATE USER docker WITH SUPERUSER PASSWORD 'docker';" &&\
createdb -O docker docker
# Adjust PostgreSQL configuration so that remote connections to the
# database are possible.
RUN echo "host all all 0.0.0.0/0 md5" >> /etc/postgresql/9.3/main/pg_hba.conf
# And add ``listen_addresses`` to ``/etc/postgresql/9.3/main/postgresql.conf``
RUN echo "listen_addresses='*'" >> /etc/postgresql/9.3/main/postgresql.conf
ENV PG_VERSION 9.3
ENV PGDATA /var/lib/postgresql/$PG_VERSION/main
ENV PGRUN /var/run/postgresql
# Expose the PostgreSQL port
EXPOSE 5432
EXPOSE 5000
# Add VOLUMEs to allow backup of config, logs and databases
VOLUME ["/etc/postgresql", "/var/log/postgresql", "/var/lib/postgresql"]
ADD . /epimobile
WORKDIR /epimobile
USER root
ADD /sudoers.txt /etc/sudoers
RUN chmod 440 /etc/sudoers
RUN sudo chmod -R 0777 src/bioinfo/data/ebov/
RUN sudo chmod -R 0777 src/bioinfo/
ENV DATABASE_NAME epimobile
ENV POSTGRESQL_USER postgres
USER postgres
# Set the default command to run when starting the container
CMD sh entrypoint.sh