Adding dockerfiles and docker documentation

doc/dev.org

@@ -469,3 +469,63 @@ make functional
 
     You're done! You can now install the debian package with:
     $ sudo dpkg -i path/to/package
+
+* Docker
+** Building the necessary images
+  The vidjil docker image is built on an Ubuntu image equipped with systemd.
+  This is a custom image for which the Dockerfile can be found in
+  docker/ubuntu_systemd.
+  In order to build the vidjil_ubuntu image, simply run
+    $ docker build -t ubuntu_systemd .
+
+  from the ubuntu_systemd directory. And then
+    $ docker build -t vidjil_ubuntu .
+
+
+** Starting a Vidjil docker environment
+   Traditionnally the Vidjil Team uses a MySQL database to store user data,
+   so in this guide we will cover setting up a MySQL Docker alongside the Vidjil Docker.
+   
+   Start the mysql container. If the tagged version is not available locally it will be pulled automatically:
+     $ docker run --name <mysql-name> -e MYSQL_ROOT_PASSWORD=<my-secret-pw> -d mysql/mysql-server:<tag>
+
+   Get the container's ip address:
+     $ docker inspect <mysql-name> | grep -i ip
+
+   Setup the vidjil databse:
+     $ mysql -h <container-ip> -u root -p
+     $ create database <vidjil-database>;
+     $ create user <vidjil-user>;
+     $ grant all on <vidjil-database>.* to '<vidjil-user>'@'%';
+     $ set password for '<vidjil-user>'@'%' = PASSWORD('<vidjil-user-password>');
+
+   Exit the MySQL interface and edit your local defs.py file to match the newly created database:
+     $ DB_ADDRESS = 'mysql://<vidjil-user>:<vidjil-user-password>@<mysql-conainer-ip>/<vidjil-database>'
+
+   Start the vidjil Docker:
+     $ docker run --name <vidjil-container-name>\
+                  --link <mysql-name>:mysql\
+                  --privileged\
+                  -d\
+                  -v /sys/fs/cgroup:/sys/fs/cgroup:ro\
+                  -v <path-to-defs>:/etc/vidjil/defs.py\
+                  -p 80:80\
+                  -p 443:443\
+                  vidjil_ubuntu
+
+   Make sure it works:
+     $ curl http://localhost/browser
+     $ curl https://localhost/vidjil
+
+** Configuring the Vidjil container
+   Should you wish to further customise your vidjil environment, most configuration files are located in /etc/vidjil/.
+   Here is a list of thos files:
+     apache_web2py                       configuration required when running vidjil with apache2
+     conf.js                             contains various variables for the vidjil browser
+     defs.py                             contains various variables for the vidjil server
+     nginx_gzip.conf                     configuration for gzip in nginx
+     nginx_gzip_static.conf              same as the previous but for static ressources
+     nginx_web2py                        configuration required when running vidjil with nginx
+     systemd_fuse_server.service         systemd service that starts the vidjil fuse server
+     systemd_web2py_scheduler.service    systemd service that starts the vidjil scheduler workers
+     uwsgi.ini                           configuration required to run vidjil with uwsgi

docker/ubuntu_systemd/Dockerfile

+FROM ubuntu:16.04
+ENV container docker
+ENV LC_ALL C
+ENV DEBIAN_FRONTEND noninteractive
+RUN echo 'APT::Install-Recommends "0"; \n\
+APT::Get::Assume-Yes "true"; \n\
+APT::Get::force-yes "true"; \n\
+APT::Install-Suggests "0";' > /etc/apt/apt.conf.d/01buildconfig
+RUN mkdir -p  /etc/apt/sources.d/
+RUN echo "deb mirror://mirrors.ubuntu.com/mirrors.txt vivid main restricted universe multiverse \n\
+deb mirror://mirrors.ubuntu.com/mirrors.txt vivid-updates main restricted universe multiverse \n\
+deb mirror://mirrors.ubuntu.com/mirrors.txt vivid-backports main restricted universe multiverse \n\
+deb mirror://mirrors.ubuntu.com/mirrors.txt vivid-security main restricted universe multiverse" > /etc/apt/sources.d/ubuntu-mirrors.list
+RUN apt-get update && apt-get install systemd
+RUN (cd /lib/systemd/system/sysinit.target.wants/; for i in *; do [ $i == systemd-tmpfiles-setup.service  ] || rm -f $i; done); \
+rm -f /lib/systemd/system/multi-user.target.wants/*;\
+rm -f /etc/systemd/system/*.wants/*;\
+rm -f /lib/systemd/system/local-fs.target.wants/*; \
+rm -f /lib/systemd/system/sockets.target.wants/*udev*; \
+rm -f /lib/systemd/system/sockets.target.wants/*initctl*; \
+rm -f /lib/systemd/system/basic.target.wants/*;\
+rm -f /lib/systemd/system/anaconda.target.wants/*; \
+rm -f /lib/systemd/system/plymouth*; \
+rm -f /lib/systemd/system/systemd-update-utmp*;
+RUN systemctl set-default multi-user.target
+ENV init /lib/systemd/systemd
+VOLUME [ "/sys/fs/cgroup"  ]
+# docker run -it --privileged=true -v /sys/fs/cgroup:/sys/fs/cgroup:ro 444c127c995b /lib/systemd/systemd systemd.unit=emergency.service
+ENTRYPOINT ["/lib/systemd/systemd"]
+CMD ["systemd.unit=emergency.service"]

docker/vidjil_ubuntu/Dockerfile

+from ubuntu_systemd
+
+label version="1.0"
+label description="An Ubuntu based docker image which comes \
+with a full installation of the Vidjil algoright and browser/server."
+
+run apt-get update
+run apt-get -y -q install apt-utils sudo curl nginx-full
+
+run echo deb http://apt.vidjil.org:8080/archive sid/all/ >> /etc/apt/sources.list
+run echo deb http://apt.vidjil.org:8080/archive sid/amd64/ >> /etc/apt/sources.list
+run echo deb http://apt.vidjil.org:8080/archive wheezy/all/ >> /etc/apt/sources.list
+run echo deb http://apt.vidjil.org:8080/archive wheezy/amd64/ >> /etc/apt/sources.list
+
+# Install Postfix. Shamelessly stolen from https://github.com/noteed/docker-postfix/blob/master/Dockerfile
+run echo "postfix postfix/main_mailer_type string Internet site" > preseed.txt
+run echo "postfix postfix/mailname string mail.example.com" >> preseed.txt
+# Use Mailbox format.
+run debconf-set-selections preseed.txt
+run DEBIAN_FRONTEND=noninteractive apt-get install -q -y postfix
+
+run postconf -e myhostname=mail.example.com
+run postconf -e mydestination="mail.example.com, example.com, localhost.localdomain, localhost"
+run postconf -e mail_spool_directory="/var/spool/mail/"
+run postconf -e mailbox_command=""
+
+run echo "vidjil-server vidjil/reconfigure-webserver string nginx" > preseed.txt
+run echo "vidjil-server vidjil/restart-webserver boolean true" >> preseed.txt
+run echo "vidjil-server vidjil/configure-startup string systemd" >> preseed.txt
+run echo "vidjil-server vidjil/start-services boolean false" >> preseed.txt
+run echo "vidjil-server vidjil/web2py-password string VidjilAdm1n" >> preseed.txt
+run echo "vidjil-server vidjil/ssl-country string AU" >> preseed.txt
+run echo "vidjil-server vidjil/ssl-state string Some-State" >> preseed.txt
+run echo "vidjil-server vidjil/ssl-locality string Some-Locality" >> preseed.txt
+run echo "vidjil-server vidjil/ssl-organisation string Internet Widgits Pty Ltd" >> preseed.txt
+run echo "vidjil-server vidjil/ssl-section string Some-Section" >> preseed.txt
+run echo "vidjil-server vidjil/ssl-name string VidjilTeam" >> preseed.txt
+run echo "vidjil-server vidjil/ssl-email string team@vidjil.org" >> preseed.txt
+
+run debconf-set-selections preseed.txt
+run echo 91.121.76.104 apt.vidjil.org >> /etc/hosts ;\
+ gpg --recv-key --keyserver apt.vidjil.org 9187987418E1A625 ;\
+ apt-get update ;\
+ DEBIAN_FRONTEND=noninteractive apt-get -y -q --allow-unauthenticated install vidjil-archive-keyring ;\
+ apt-get update ;\
+ DEBIAN_FRONTEND=noninteractive apt-get install -y -q --allow-unauthenticated vidjil-server
+
+run cd /usr/share/vidjil/germline && make
+run cd /usr/share/web2py && chown -R www-data:www-data .
+
+run systemctl enable web2py.scheduler.service fuse.server.service
+
+cmd ["/bin/systemctl", "start", "nginx.service"]
+cmd ["/bin/systemctl", "start", "uwsgi.service"]
+
+expose 80
+expose 443
+cmd ["/usr/sbin/init"]