Docker

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Official web page http://docker.io.

Docker is both a client and a server: the server is a daemon that runs on Linux. The normal approach was that you used docker on the same server the daemon was running on - however it was possible to connect the docker client to a remote docker daemon.

Contents

Installation

Which OS to install?

Containers vs virtual machines

OS containers vs application containers

Differences:

  • OS containers: LXC, OpenVZ, Linux VServer, BSD Jails and Solaris zones. The container acts as VPS.
  • App containers: Docker, Rocket. The container acts as an application.

Current release version

Without sudo, Post-installation

To use docker without sudo, follow the instruction on the official guide.

# Add the docker group if it doesn't already exist.
# sudo groupadd docker

# Add your user to the docker group.
sudo usermod -aG docker $USER

# Log out and log in

CentOS

https://docs.docker.com/engine/installation/linux/docker-ce/centos/

Boot2Docker

For Windows and OS operation systems, we have to use Boot2Docker. Boot2Docker is a local virtual machine with its own network interface and IP address. To find the Boot2Docker IP address you can check the value of the DOCKER_HOST environment variable. You're be prompted to set this variable when you start or install Boot2Docker the first time. You can find the IP address by running boot2docker ip command.

Note that since Windows and OS X don't share a file system as Linux, the command 'docker run' with '-v' flag to mount a local directory into a Docker container will not work with Boot2Docker release prior to 1.3. The support for volumes is now available for OS X but is not yet present for Windows with the release of Boot2Docker 1.3.

Windows

Docker can be run on Windows 10 Pro as a native application; see

The information below is based on running Docker on Windows 7.1 and 8. Your processor needs to support hardware virtualization.

  • Windows Installer includes msys-git, Virtualbox, Boot2Docker-cli management tool and Boot2Docker ISO.
  • Installation instruction for Windows OS. It will install Boot2Docker management tool with the boot2docker iso (based on Tiny Core Linux), Virtualbox and MYSYS-git UNIX tools.
  • Docker needs Admin right to be installed. However, Virtualbox can be installed by user's account.
  • If the installer detects a version of VirtualBox installed, the VirtualBox checkbox will not be checked by default (Windows OS). The VirtualBox cannot be used anymore after updating my VB from 4.3.18 to 4.3.20. The error may be related to Windows update according to Virtualbox forum.
Error in supR3HardenedWinReSpawn
  • Note that boot2docker cannot be installed/run inside a Windows guest machine. See this post and my Virtualbox wiki here. If we try to launch boot2docker-vm from Virtualbox, we will see a message "This kernel requires an x86-64 CPU, but only detected an i686 CPU."
  • After I switch back to an old version of virtualbox, every thing works again. I can even install Docker successfully.
    • Boot2Docker Start icon cannot be run directly because Notepad++ will automatically open it. A possible solution is to go to control panel and change default program for .sh file from Notepad++ to C:\Program Files (x86)\Git\bin\bash.exe.
    • The above step does not work well since a terminal appears and disappears quickly.
    • A working approach is to open Git Bash from Start menu. And run /c/Program Files/Boot2DockerforWindows/start.sh (or boot2docker start or boot2docer init)
    • A new VM called 'boot2docker-vm' will be created (we can open VirtualBox Manager to check). But I got an error error in run: Failed to start machine "boot2docker-vm" (run again with -v for details). The VM has an error on Network>Adapter2>VirtualBox Host-Only Ethernet Adapter #2. So I open the setting of <boot2docker-vm>, go to Network > Adapter 2 and change the dropdown list of Name from VirtualBox Host-Only Ethernet Adapter #2 to VirtualBox Host-Only Ethernet Adapter.
    • Now it works either I directly click boot2docker-vm VM from VB Manager or use the command start.sh from Git Bash.

Boot2docker-vm.png

$ # boot2docker is in the PATH variable, so there is not need to cd to the folder.
$ boot2docker start
initializing...
Virtual machine boot2docker-vm already exists

starting...
Waiting for VM and Docker daemon to start...
........o
Started.
Writing c:\Users\brb\.boot2docker\certs\boot2docker-vm\ca.pem
Writing c:\Users\brb\.boot2docker\certs\boot2docker-vm\cert.pem
Writing c:\Users\brb\.boot2docker\certs\boot2docker-vm\key.pem
Docker client does not run on Windows for now. Please use
    "c:\Program files\Boot2Docker for Windows\boot2docker.exe" ssh
to SSH into the VM instead.


192.168.56.101
connecting...
                        ##        .
                  ## ## ##       ==
               ## ## ## ##      ===
           /""""""""""""""""\___/ ===
      ~~~ {~~ ~~~~ ~~~ ~~~~ ~~ ~ /  ===- ~~~
           \______ o          __/
             \    \        __/
              \____\______/
 _                 _   ____     _            _
| |__   ___   ___ | |_|___ \ __| | ___   ___| | _____ _ __
| '_ \ / _ \ / _ \| __| __) / _` |/ _ \ / __| |/ / _ \ '__|
| |_) | (_) | (_) | |_ / __/ (_| | (_) | (__|   <  __/ |
|_.__/ \___/ \___/ \__|_____\__,_|\___/ \___|_|\_\___|_|
Boot2Docker version 1.4.1, build master : 86f7ec8 - Tue Dec 16 23:11:29 UTC 2014

Docker version 1.4.1, build 5bc2ff8
docker@boot2docker:~$ docker
Usage: docker [OPTIONS] COMMAND [arg...]

A self-sufficient runtime for linux containers.

Options:
  --api-enable-cors=false                      Enable CORS headers in the remote
 API
  -b, --bridge=""                              Attach containers to a pre-existi
ng network bridge
...
Run 'docker COMMAND --help' for more information on a command.
docker@boot2docker:~$ docker run hello-world
Unable to find image 'hello-world:latest' locally
hello-world:latest: The image you are pulling has been verified
511136ea3c5a: Pull complete
31cbccb51277: Pull complete
e45a5af57b00: Pull complete
Status: Downloaded newer image for hello-world:latest
Hello from Docker.
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (Assuming it was not already locally available.)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

For more examples and ideas, visit:
 http://docs.docker.com/userguide/

docker@boot2docker:~$ ls
boot2docker, please format-me
docker@boot2docker:~$ pwd
/home/docker
docker@boot2docker:~$ ls /
bin/     dev/     home/    lib/     mnt/     proc/    run/     sys/     usr/
c/       etc/     init     linuxrc  opt/     root/    sbin/    tmp      var/

docker@boot2docker:~$ docker run hello-world
Hello from Docker.
This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:
 1. The Docker client contacted the Docker daemon.
 2. The Docker daemon pulled the "hello-world" image from the Docker Hub.
    (Assuming it was not already locally available.)
 3. The Docker daemon created a new container from that image which runs the
    executable that produces the output you are currently reading.
 4. The Docker daemon streamed that output to the Docker client, which sent it
    to your terminal.

To try something more ambitious, you can run an Ubuntu container with:
 $ docker run -it ubuntu bash

For more examples and ideas, visit:
 http://docs.docker.com/userguide/
docker@boot2docker:~$
docker@boot2docker:~$
docker@boot2docker:~$
docker@boot2docker:~$ docker run -it ubuntu bash
Unable to find image 'ubuntu:latest' locally
ubuntu:latest: The image you are pulling has been verified
53f858aaaf03: Pull complete
837339b91538: Pull complete
615c102e2290: Pull complete
b39b81afc8ca: Pull complete
511136ea3c5a: Already exists
Status: Downloaded newer image for ubuntu:latest


root@ea7e3289a01a:/# pwd
/
root@ea7e3289a01a:/# df -h
Filesystem      Size  Used Avail Use% Mounted on
rootfs           19G  269M   17G   2% /
none             19G  269M   17G   2% /
tmpfs          1005M     0 1005M   0% /dev
shm              64M     0   64M   0% /dev/shm
/dev/sda1        19G  269M   17G   2% /etc/hosts
tmpfs          1005M     0 1005M   0% /proc/kcore
root@ea7e3289a01a:/# ls
bin   dev  home  lib64  mnt  proc  run   srv  tmp  var
boot  etc  lib   media  opt  root  sbin  sys  usr
root@ea7e3289a01a:/# exit
exit


docker@boot2docker:~$ pwd
/home/docker
docker@boot2docker:~$ ls
boot2docker, please format-me
docker@boot2docker:~$ exit
[Press any key to exit]

brb@NCI-01825357 /c/Program files/Boot2Docker for Windows
$ boot2docker down

brb@NCI-01825357 /c/Program files/Boot2Docker for Windows
$
$ boot2docker --help
Usage: c:\Program files\Boot2Docker for Windows\boot2docker.exe [<options>] <command> [<args>]

Boot2Docker management utility.

Commands:
   init                Create a new Boot2Docker VM.
   up|start|boot       Start VM from any states.
   ssh [ssh-command]   Login to VM via SSH.
   save|suspend        Suspend VM and save state to disk.
   down|stop|halt      Gracefully shutdown the VM.
   restart             Gracefully reboot the VM.
   poweroff            Forcefully power off the VM (may corrupt disk image).
   reset               Forcefully power cycle the VM (may corrupt disk image).
   delete|destroy      Delete Boot2Docker VM and its disk image.
   config|cfg          Show selected profile file settings.
   info                Display detailed information of VM.
   ip                  Display the IP address of the VM's Host-only network.
   shellinit           Display the shell commands to set up the Docker client.
   status              Display current state of VM.
   download            Download Boot2Docker ISO image.
   upgrade             Upgrade the Boot2Docker ISO image (restart if running).
   version             Display version information.

Options:
      --basevmdk="": Path to VMDK to use as base for persistent partition
      --clobber=false: overwrite Docker client binary on boot2docker upgrade
      --dhcp=true: enable VirtualBox host-only network DHCP.
      --dhcpip=192.168.59.99: VirtualBox host-only network DHCP server address.
....
  -v, --verbose=false: display verbose command invocations.
      --vm="boot2docker-vm": virtual machine name.
      --waittime=300: Time in milliseconds to wait between port knocking retries during 'start'
error in run: config error: pflag: help requested

brb@NCI-01825357 /c/Program files/Boot2Docker for Windows

The big picture


                           start.sh                      docker run -it ubuntu bash
Git Bash Git Bash         ---------->  boot2docker-vm       ------------->   ubuntu
                                   docker@boot2docker:
   <-------               <----------                       <------------- 
   boot2docker down           exit                                 exit
   (shutdown boot2docker) (boot2docker-vm is still on)
    |
    |
    |  boot2docker up (start boot2docker)
    |
    |  boot2docker ssh (log into docker acct)
    |
    v
   boot2docker-vm
   docker@boot2docker

Increase boot2docker vmdk space

https://docs.docker.com/articles/b2d_volume_resize/

Install utilities in Boot2docker VM

http://blog.tutum.co/2014/11/05/how-to-use-docker-on-windows/

For example, to install cifs-utils,

wget http://distro.ibiblio.org/tinycorelinux/5.x/x86/tcz/cifs-utils.tcz
tce-load -i cifs-utils.tcz

Mac

If you have Mac, you don't have to use boot2docker (iso & its management tool). You can use other Linux which comes with docker pre-installed. See this post.

Odroid

  • See Odroid magazine 2015 January and 2015 February. Note that the current versions of Docker and Docker Hub are not aware of the architecture for which the image has been built. All standard images are intended for the x86 architecture, and the autobuild feature offered by the Docker registry is only available for x86.

GUI/TUI interface manager

Dry

Dry – An Interactive CLI Manager For Docker Containers. The TUI is built on top of termui; a cross-platform, easy-to-compile, and fully-customizable terminal dashboard. It is inspired by blessed-contrib, but purely in Go.

Rancher

$ sudo apt-get install ufw
$ sudo ufw allow 4500/udp
$ sudo ufw allow 500/udp
  • discoposse.com
    • Part 1 Installing Rancher and Setting Access Control
    • Part 2 Adding a Docker Host to Rancher
    • Part 3 Adding the DockerHub to our Rancher Registry
    • Part 4 Using the Catalog Example with GlusterFS

Seagull

https://youtu.be/TuT5gb8oRw8

docker run -d -p 127.0.0.1:10086:10086 -v /var/run/docker.sock:/var/run/docker.sock tobegit3hub/seagull

The only issue is there is no username/password to protect other people to access the web GUI. The solution of binding to localhost to restrict the access does not work for remote administration.

That is, the tool is suitable for home use.

Kitematic

Available for Mac OS X 10.8+ and Windows 7+ (64-bit) and Ubuntu. https://github.com/docker/kitematic/releases/

Run containers through a simple, yet powerful graphical user interface.

A Share your Shiny Apps with Docker and Kitematic!

Portainer

https://portainer.readthedocs.io/en/stable/deployment.html#manage-a-new-docker-environment

sudo docker run -d -p 9000:9000 -v /var/run/docker.sock:/var/run/docker.sock -v portainer_data:/data portainer/portainer -H tcp://192.168.1.98:2375

Go to http://192.168.1.98:9000. But I still don't see the other containers that are running now:(

DockerUI (Deprecated, Development continues at Portainer)

A quick start:

1. Run:

docker run -d -p 9000:9000 --privileged -v /var/run/docker.sock:/var/run/docker.sock dockerui/dockerui

where -v means to bind mount a volume.

2. Open your browser to http://<dockerd host ip>:9000

Shipyard (retired)

Usage

Basics, docs, cheatsheet

Note that we need sudo is needed unless it is on a Mac OS.

If docker cannot find an image, it will try to pull it from its repository.

$ sudo docker run -it ubuntu /bin/bash
Unable to find image 'ubuntu' locally
Pulling repository ubuntu
04c5d3b7b065: Download complete 
511136ea3c5a: Download complete 
c7b7c6419568: Download complete 
70c8faa62a44: Download complete 
d735006ad9c1: Download complete 
root@ec83b3ac878d:/# 
purpose command
run a container docker container run -d -p 80:80 httpd
list running cotainer docker container ls
view logs of Docker container docker container logs cranky_cori
identify Docker container process? docker container top cranky_cori
stop Docker container? docker container stop cranky_cori
list stopped or not running Docker containers docker container ls -a
start Docker container docker container start c46f2e9e4690
remove Docker container docker container rm cranky_cori
list Docker images docker images
remove Docker image docker rmi iman/touch

Restart docker daemon

When I try the Chap5 > Continuous integration (Jenkins) of the Docker Book, I found I cannot stop/kill the container. See others' report here. The solution is to restart the docker daemon.

sudo service docker start

After that, I can stop and rm the container.

sudo docker stop jenkins
sudo docker rm jenkins
sudo docker ps -a

images vs containers

$ sudo docker images
REPOSITORY                     TAG                 IMAGE ID            CREATED              VIRTUAL SIZE
iman                           latest              6e0f5644b2fd        About a minute ago   460.4 MB
iman/touch                     latest              77b9ac5951c2        4 minutes ago        460.4 MB
<none>                         <none>              aaa75e64ddf0        5 weeks ago          188.3 MB
ouruser/sinatra                v2                  ea8c9f407a8d        5 weeks ago          447 MB
ubuntu                         14.04               ed5a78b7b42b        5 weeks ago          188.3 MB
ubuntu                         latest              ed5a78b7b42b        5 weeks ago          188.3 MB
eddelbuettel/docker-ubuntu-r   add-r-devel-san     3c19d078c5d9        3 months ago         460.4 MB
hello-world                    latest              ef872312fe1b        4 months ago         910 B
training/sinatra               latest              f0f4ab557f95        8 months ago         447 MB

$ sudo docker ps -a
CONTAINER ID IMAGE                                          COMMAND              CREATED        STATUS                   PORTS NAMES
8fbdbcdb5126 iman/touch:latest                              "/bin/bash"          2 minutes ago  Exited (0) 2 minutes ago       thirsty_engelbart   
dc9e82f2c00a eddelbuettel/docker-ubuntu-r:add-r-devel-san   "/bin/bash"          9 minutes ago  Exited (0) 3 minutes ago       kickass_bardeen     
532a90f36aa8 eddelbuettel/docker-ubuntu-r:add-r-devel-san   "/bin/bash"          18 hours ago   Exited (0) 18 hours ago        happy_lalande       
7634024ee0bf eddelbuettel/docker-ubuntu-r:add-r-devel-san   "/bin/bash"          18 hours ago   Exited (0) 18 hours ago        insane_mclean       
14034a9720cb eddelbuettel/docker-ubuntu-r:add-r-devel-san   "/bin/bash"          18 hours ago   Exited (0) 18 hours ago        naughty_lumiere     
ca90954628db eddelbuettel/docker-ubuntu-r:add-r-devel-san   "/bin/bash"          19 hours ago   Exited (130) 18 hours ago      sick_hawking        
8bbdcb7c339f eddelbuettel/docker-ubuntu-r:add-r-devel-san   "/bin/bash"          19 hours ago   Exited (0) 19 hours ago        modest_davinci      
e8e24f80f0dd aaa75e64ddf0                                   "/bin/sh -c 'apt-get 5 weeks ago    Exited (100) 5 weeks ago       berserk_hodgkin     
d41959e0eb55 aaa75e64ddf0                                   "/bin/sh -c 'apt-get 5 weeks ago    Exited (100) 5 weeks ago       jovial_curie        
b408c0e2805b aaa75e64ddf0                                   "/bin/sh -c 'apt-get 5 weeks ago    Exited (100) 5 weeks ago       lonely_tesla        
72a551e4b492 ouruser/sinatra:v2                             "/bin/bash"          5 weeks ago    Exited (0) 5 weeks ago         jolly_meitner       
75fd6cc4658b training/sinatra:latest                        "/bin/bash"          5 weeks ago    Exited (0) 5 weeks ago         evil_yalow          
cc8886f5a02e training/sinatra:latest                        "/bin/bash"          5 weeks ago    Exited (130) 5 weeks ago       elegant_curie       
0585e4f5fecd eddelbuettel/docker-ubuntu-r:add-r-devel-san   "/bin/bash"          5 weeks ago    Exited (0) 5 weeks ago         elated_euclid       
brb@brbweb4:~/Downloads$ 

When we want to delete a container, we use the container's CONTAINER ID or NAME (last column output from docker ps -a). But when we want to delete an image, we use the image's REPOSITORY or IMAGE ID (2nd column output from docker images)

$ sudo docker rm thirsty_engelbart  # iman/touch
$ sudo docker rm dc9e82f2c00a       # eddelbuettel/docker-ubuntu-r:add-r-devel-san
$ sudo docker ps -a   # check to see the container is gone now

$ sudo docker rmi 6e0f5644b2fd
$ sudo docker rmi iman/touch
$ sudo docker images  # check to see the images are gone now

Docker command line / CLI

$ docker

Usage:	docker COMMAND

A self-sufficient runtime for containers

Options:
      --config string      Location of client config files (default "/home/brb/.docker")
  -D, --debug              Enable debug mode
  -H, --host list          Daemon socket(s) to connect to
  -l, --log-level string   Set the logging level ("debug"|"info"|"warn"|"error"|"fatal") (default "info")
      --tls                Use TLS; implied by --tlsverify
      --tlscacert string   Trust certs signed only by this CA (default "/home/brb/.docker/ca.pem")
      --tlscert string     Path to TLS certificate file (default "/home/brb/.docker/cert.pem")
      --tlskey string      Path to TLS key file (default "/home/brb/.docker/key.pem")
      --tlsverify          Use TLS and verify the remote
  -v, --version            Print version information and quit

Management Commands:
  config      Manage Docker configs
  container   Manage containers
  image       Manage images
  network     Manage networks
  node        Manage Swarm nodes
  plugin      Manage plugins
  secret      Manage Docker secrets
  service     Manage services
  swarm       Manage Swarm
  system      Manage Docker
  trust       Manage trust on Docker images
  volume      Manage volumes

Commands:
  attach      Attach local standard input, output, and error streams to a running container
  build       Build an image from a Dockerfile
  commit      Create a new image from a container's changes
  cp          Copy files/folders between a container and the local filesystem
  create      Create a new container
  diff        Inspect changes to files or directories on a container's filesystem
  events      Get real time events from the server
  exec        Run a command in a running container
  export      Export a container's filesystem as a tar archive
  history     Show the history of an image
  images      List images
  import      Import the contents from a tarball to create a filesystem image
  info        Display system-wide information
  inspect     Return low-level information on Docker objects
  kill        Kill one or more running containers
  load        Load an image from a tar archive or STDIN
  login       Log in to a Docker registry
  logout      Log out from a Docker registry
  logs        Fetch the logs of a container
  pause       Pause all processes within one or more containers
  port        List port mappings or a specific mapping for the container
  ps          List containers
  pull        Pull an image or a repository from a registry
  push        Push an image or a repository to a registry
  rename      Rename a container
  restart     Restart one or more containers
  rm          Remove one or more containers
  rmi         Remove one or more images
  run         Run a command in a new container
  save        Save one or more images to a tar archive (streamed to STDOUT by default)
  search      Search the Docker Hub for images
  start       Start one or more stopped containers
  stats       Display a live stream of container(s) resource usage statistics
  stop        Stop one or more running containers
  tag         Create a tag TARGET_IMAGE that refers to SOURCE_IMAGE
  top         Display the running processes of a container
  unpause     Unpause all processes within one or more containers
  update      Update configuration of one or more containers
  version     Show the Docker version information
  wait        Block until one or more containers stop, then print their exit codes

Run 'docker COMMAND --help' for more information on a command.

A brief intro to docker virtualization

docker search --help
docker search redis
docker search -s 100 redis
docker pull --help
docker pull ubuntu # download all versions of ubuntu
docker images    # available local container images
docker pull centos:latest
docker run --help
cat /etc/issue   # look at the current distr name before running docker
docker run -it centos:latest /bin/bash
                 # create a container & execute as a sudo

cat /etc/redhat-release
yum
cd /home
touch temp.txt
ls
exit

docker ps   # current running processes
docker ps -a # show all processes including closed
docker restart c85850ed0e13
docker ps   # container c85850ed0e13 is running
docker attach c85850ed0e13 # log into the system

ls /home
exit

docker ps -a
docker rm c85850ed0e13 # delete the container

Note: Following the discussion, using attach can only launch one instance of shell. If we use exec, we can launch multiple instances.

sudo docker exec -i -t c85850ed0e13 bash #by ID
or
$ sudo docker exec -i -t loving_heisenberg bash #by Name

docker pull

$ docker pull ubuntu:zesty
$ docker run -ti --rm ubuntu:zesty /bin/bash 
# lsb_release -a         
bash: lsb_release: command not found
# cat /etc/*release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=17.04
DISTRIB_CODENAME=zesty
DISTRIB_DESCRIPTION="Ubuntu 17.04"
NAME="Ubuntu"
VERSION="17.04 (Zesty Zapus)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 17.04"
VERSION_ID="17.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=zesty
UBUNTU_CODENAME=zesty

Dockerizing Applications/Detached mode

$ sudo docker run -d --name insane_babbage ubuntu:14.04 /bin/sh -c "while true; do echo hello world; sleep 1; done"
$ sudo docker ps -l
$ sudo docker logs insane_babbage
$ sudo docker stop insane_babbage
$ sudo docker ps

The -d flag tells Docker to run the container and put it in the background, to daemonize it.

According to https://docs.docker.com/engine/reference/run/#detached-vs-foreground, containers started in detached mode exit when the root process used to run the container exits, unless you also specify the --rm option. If you use -d with --rm, the container is removed when it exits or when the daemon exits, whichever happens first.

Auto restart after reboot

https://stackoverflow.com/questions/18786054/how-to-auto-restart-a-docker-container-after-a-reboot-in-coreos

Add a --restart=always parameter. See the following

Working with Containers

$ sudo docker run -i -t ubuntu /bin/bash
$ sudo docker version
$ sudo docker
$ sudo docker attach --help

Running a Web Application

$ sudo docker run -d -P training/webapp python app.py

Alpine linux is 6MB. It is a good OS to run a web application. See the demo here.

Viewing our Web Application Container

$ sudo docker ps -l
$ sudo docker run -d -p 5000:5000 training/webapp python app.py

Container networking

Network Port Shortcut

$ sudo docker port nostalgic_morse 5000

Viewing the Web Application's Logs

$ sudo docker logs -f nostalgic_morse

Looking at our Web Application Container's processes

$ sudo docker top nostalgic_morse

Inspecting our Web Application Container

$ sudo docker inspect nostalgic_morse

Obtain the container's IP address, log into a running server

$ docker inspect <container id> | grep "IPAddress"

Then to log into a running server, use

$ docker exec -it <contianer id> bash

Restart a Container

$ sudo docker start nostalgic_morse
OR
$ sudo docker restart nostalgic_morse

Know the container size

docker ps -s

Meaning of two sizes

  • The "size" information shows the amount of data (on disk) that is used for the writable layer of each container
  • The "virtual size" is the amount of disk-space used for the read-only image data used by the container.

Removing our Web Application Container

$ sudo docker stop nostalgic_morse
$ sudo docker rm nostalgic_morse

Note: Always remember that deleting a container is final!

Dockerize an SSH service

https://docs.docker.com/engine/examples/running_ssh_service/#environment-variables

Remove old docker containers

This post on stackoverflow.com.

$ sudo docker ps -a | grep 'weeks ago' | awk '{print $1}' | xargs --no-run-if-empty sudo docker rm

Similarly to remove all exited containers

$ sudo docker ps -a | grep Exit | awk '{print $1}' | xargs sudo docker rm

To kill/stop (not delete) all running containers

$ sudo docker kill $(sudo docker ps -q)

To delete all stopped containers

$ sudo docker rm $(sudo docker ps -a -q)
OR
$ sudo docker rm `sudo docker ps -a -q`

It is also helpful to create bash aliases for these commands by editing ~/.bash_aliases file.

Work with container images

Note that it is better/necessary to put the Dockerfile in an empty directory to avoid the problem of taking a long time to build the image (sending build context to Docker daemon ...GB ) since it will grab files from the current directory.

sudo docker search sinatra
sudo docker pull training/sinatra
sudo docker run -t -i training/sinatra /bin/bash
sudo docker commit -m="Added json gem" -a="Kate Smith" 0b2616b0e5a8 ouruser/sinatra:v2
sudo docker images

mkdir sinatra
cd sinatra
touch Dockerfile
sudo docker build -t="ouruser/sinatra:v2" .
sudo docker push ouruser/sinatra
sudo docker rmi training/sinatra
  • The above exercise works on my home computer (64-bit Ubuntu 12.04). However when I want to remove an image, I need to do something extra.
$ sudo docker rmi training/sinatra
Error response from daemon: Conflict, cannot delete f0f4ab557f95 because the container bc5175998df3 is using it, use -f to force
FATA[0000] Error: failed to remove one or more images 
$ sudo docker ps 
CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES
$ 
$ sudo docker rm $(sudo docker ps -aq)
bc5175998df3
b97cb467529c
$ sudo docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
ouruser/sinatra     v2                  bd6395724621        9 minutes ago       316.3 MB
ubuntu              14.04               ed5a78b7b42b        4 days ago          188.3 MB
ubuntu              latest              ed5a78b7b42b        4 days ago          188.3 MB
training/sinatra    latest              f0f4ab557f95        6 months ago        447 MB
$ sudo docker rmi training/sinatra
Untagged: training/sinatra:latest
Deleted: f0f4ab557f954f3e04177663a3af90e88641bcdcce1f02ac900dbd9768ef4945
...
Deleted: 3e76c0a80540a0d36493ae7110796fc92f559a191454e3ac19c1d4c650bdd9e0
$ sudo docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
ouruser/sinatra     v2                  bd6395724621        10 minutes ago      316.3 MB
ubuntu              latest              ed5a78b7b42b        4 days ago          188.3 MB
ubuntu              14.04               ed5a78b7b42b        4 days ago          188.3 MB
$ sudo docker rmi ouruser/sinatra
Error response from daemon: No such image: ouruser/sinatra:latest
FATA[0000] Error: failed to remove one or more images   
$ sudo docker rmi ouruser/sinatra:v2
Untagged: ouruser/sinatra:v2
Deleted: bd6395724621a89384ec58c116ce113ae8371f31f20f0adc540bbc76c6049d12
...
Deleted: 41ce107b0a0bb6a70834477e3b550386fc453de363d8a20f0579df055e9ece50
  • I get an error when I try to launch sinatra on my 32-bit ubuntu (Docker can only be installed through apt-get on 32-bit)
$ sudo docker run -t -i training/sinatra /bin/bash
2014/12/31 02:43:26 exec format error
  • I get lots of errors when I run docker build command on my 64-bit Ubuntu.
$ sudo docker build -t="ouruser/sinatra:v2" .
Sending build context to Docker daemon  2.56 kB
Sending build context to Docker daemon 
Step 0 : FROM ubuntu:14.04
Pulling repository ubuntu
ed5a78b7b42b: Download complete 
511136ea3c5a: Download complete 
fe95bf7d5f50: Download complete 
9a4594fe74ea: Download complete 
8c4b1edcceea: Download complete 
 ---> ed5a78b7b42b
Step 1 : MAINTAINER Kate Smith <ksmith@example.com>
 ---> Running in 63614919cafd
 ---> 5bac5869eb36
Removing intermediate container 63614919cafd
Step 2 : RUN apt-get update && apt-get install -y ruby ruby-dev
 ---> Running in 68e8ccfa5f7c
Err http://archive.ubuntu.com trusty InRelease
  
Err http://archive.ubuntu.com trusty-updates InRelease
  
Err http://archive.ubuntu.com trusty-security InRelease
  
Err http://archive.ubuntu.com trusty Release.gpg
  Could not resolve 'archive.ubuntu.com'
Err http://archive.ubuntu.com trusty-updates Release.gpg
  Could not resolve 'archive.ubuntu.com'
Err http://archive.ubuntu.com trusty-security Release.gpg
  Could not resolve 'archive.ubuntu.com'
Reading package lists...
W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/trusty/InRelease  

W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/trusty-updates/InRelease  

W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/trusty-security/InRelease  

W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/trusty/Release.gpg  Could not resolve 'archive.ubuntu.com'

W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/trusty-updates/Release.gpg  Could not resolve 'archive.ubuntu.com'

W: Failed to fetch http://archive.ubuntu.com/ubuntu/dists/trusty-security/Release.gpg  Could not resolve 'archive.ubuntu.com'

W: Some index files failed to download. They have been ignored, or old ones used instead.
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 ruby-dev : Depends: ruby1.9.1-dev (>= 1.9.3.194-1) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
2014/12/30 16:03:21 The command [/bin/sh -c apt-get update && apt-get install -y ruby ruby-dev] returned a non-zero code: 100

Resources allocated to a container using docker?

https://stackoverflow.com/questions/16084741/how-do-i-set-resources-allocated-to-a-container-using-docker

hub.docker.com

sudo docker pull phusion/baseimage
sudo docker run -ti phusion/baseimage /bin/bash
  • https://dockerfile.github.io/ which includes dockerfiles for different purposes. The ubuntu-desktop one also works well (client needs a vnc viewer in order to see the desktop).

Set up a private Docker registry

Dockerfile

Remember to put the Dockerfile in an empty directory.

Examples of Dockerfile

How to use Dockerfile

sudo docker build -t [myname] .  

Dockerfile in One Line

FROM ubuntu

Using This simple Dockerfile and the docker command sudo docker build -t scooby_snacks . will result in

$ sudo docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
ubuntu              15.04               2427658c75a1        42 hours ago        117.5 MB
ubuntu              vivid               2427658c75a1        42 hours ago        117.5 MB
ubuntu              vivid-20150218      2427658c75a1        42 hours ago        117.5 MB
ubuntu              utopic-20150211     78949b1e1cfd        42 hours ago        194.4 MB
ubuntu              utopic              78949b1e1cfd        42 hours ago        194.4 MB
ubuntu              14.10               78949b1e1cfd        42 hours ago        194.4 MB
ubuntu              14.04               2d24f826cb16        42 hours ago        188.3 MB
ubuntu              14.04.2             2d24f826cb16        42 hours ago        188.3 MB
ubuntu              trusty              2d24f826cb16        42 hours ago        188.3 MB
ubuntu              trusty-20150218.1   2d24f826cb16        42 hours ago        188.3 MB
ubuntu              latest              2d24f826cb16        42 hours ago        188.3 MB
scooby_snacks       latest              2d24f826cb16        42 hours ago        188.3 MB
ubuntu              precise             1f80e9ca2ac3        42 hours ago        131.5 MB
ubuntu              precise-20150212    1f80e9ca2ac3        42 hours ago        131.5 MB
ubuntu              12.04.5             1f80e9ca2ac3        42 hours ago        131.5 MB
ubuntu              12.04               1f80e9ca2ac3        42 hours ago        131.5 MB
ubuntu              14.04.1             5ba9dab47459        3 weeks ago         188.3 MB
ubuntu              12.10               c5881f11ded9        8 months ago        172.2 MB
ubuntu              quantal             c5881f11ded9        8 months ago        172.2 MB
ubuntu              13.04               463ff6be4238        8 months ago        169.4 MB
ubuntu              raring              463ff6be4238        8 months ago        169.4 MB
ubuntu              13.10               195eb90b5349        8 months ago        184.7 MB
ubuntu              saucy               195eb90b5349        8 months ago        184.7 MB
ubuntu              10.04               3db9c44f4520        10 months ago       183 MB
ubuntu              lucid               3db9c44f4520        10 months ago       183 MB

Run a shell script on host

$ docker run -v /path/to/sample_script.sh:/sample_script.sh \
  --rm ubuntu bash sample_script.sh

# GATK container example
# First we log in interactive and see where is the default location (/usr in this case)
$ docker run --rm -i -t broadinstitute/gatk3:3.8-0 bash
$ cat > tmp.sh << EOF
> pwd
> ls
> java -jar GenomeAnalysisTK.jar --version
> EOF
$ docker run --rm -v $(pwd):/usr/my broadinstitute/gatk3:3.8-0 bash my/tmp.sh
# ALTERNATIVELY, WE CAN PUT OUR SCRIPT IN THE TOP DIRECTORY (Hopefully the name is not duplicated)
$ docker run --rm -v $(pwd)/tmp.sh:/tmp.sh broadinstitute/gatk3:3.8-0 bash /tmp.sh
docker run -d -v$(pwd):/my SOMEIMAGE bash 
docker exec -d Test bash /my/script.sh

Link containers together

Manage data in containers

https://docs.docker.com/userguide/dockervolumes/

Assign static iP to a container

Working with Docker hub

https://docs.docker.com/userguide/dockerrepos/

GUI apps

Misc

LXC (raw Linux containers)

LXC vs Docker

Vagrant vs Docker

Date/Time zone

docker run --rm -t -i -v /etc/localtime:/etc/localtime:ro ubuntu date

Access the internet from the container

Run the container with the '--net=host' option

sudo docker run --net=host -it ubuntu /bin/bash

Where are Docker images stored on the host machine/Location of Docker images (/etc/default/docker.io)

The default is /var/lib/docker. Three options if we are tight on the disk space.

1. Create a softlinks for the Docker data directory (/var/lib/docker) and for /var/lib/docker/tmp as described at miscellaneous-options.

2. Command line option (-v). See Where to Store Data

3. Change the default location to another place. For example,

sudo nano /etc/default/docker.io
# Add a line DOCKER_OPTS="-g /home/brb/Docker"

Then after running sudo service docker.io restart and then a simple pull sudo docker pull rocker/r-base or sudo docker run --rm -ti rocker/r-base (the Dockerfile of r-base is available on github.com, --rm option means Automatically remove the container when it exits), we will see something like this:

$ sudo docker run --rm -ti rocker/r-base
Unable to find image 'rocker/r-base:latest' locally
Pulling repository rocker/r-base
ca3e0842c8f7: Download complete 
b2601258a687: Download complete 
c47fad72b020: Download complete 
625e14fa4ae0: Download complete 
13711ce90d62: Download complete 
116733e9a647: Download complete 
616527c7a2af: Download complete 
ffcc1c0a1e17: Download complete 
6400c17017f4: Download complete 
68855631fa1e: Download complete 
6c218b542d06: Download complete 
973a399c73a9: Download complete 
Status: Downloaded newer image for rocker/r-base:latest

$ sudo docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
rocker/r-base       latest              0f9a4a6133e9        5 days ago          499.7 MB

$ sudo docker -v
Docker version 1.0.1, build 990021a

$ sudo docker -D info
Containers: 0
Images: 13
Storage Driver: aufs
 Root Dir: /home/brb/Docker/aufs
 Dirs: 13
Execution Driver: native-0.2
Kernel Version: 3.13.0-32-generic
Debug mode (server): false
Debug mode (client): true
Fds: 9
Goroutines: 10
EventsListeners: 0
Init SHA1: 6578c4a98eb5aaa1db564782fd990839ebca1b4d
Init Path: /usr/lib/docker.io/dockerinit
WARNING: No swap limit support

$ sudo cat Docker/repositories-aufs | python -mjson.tool
bash: su/repositories-aufs: No such file or directory
No JSON object could be decoded
brb@vm-1404:~$ sudo cat Docker/repositories-aufs | python -mjson.tool
{
    "Repositories": {
        "rocker/r-base": {
            "latest": "0f9a4a6133e94d2e2ae092d447cfcc5366145ab62799de1c706ac9af90ce002a"
        }
    }
}

$ sudo ls -lh Docker/graph/0f9a4a6133e94d2e2ae092d447cfcc5366145ab62799de1c706ac9af90ce002a
total 8.0K
-rw------- 1 root root 1.6K Feb 22 16:21 json
-rw------- 1 root root    1 Feb 22 16:21 layersize

$ sudo cat Docker/graph/0f9a4a6133e94d2e2ae092d447cfcc5366145ab62799de1c706ac9af90ce002a/json |  python -mjson.tool
{
    "Size": 0,
    "architecture": "amd64",
    "author": "\"Carl Boettiger and Dirk Eddelbuettel\" rocker-maintainers@eddelbuettel.com",
    "config": {
        "AttachStderr": false,
        "AttachStdin": false,
        "AttachStdout": false,
        "Cmd": [
            "R"
        ],
        "CpuShares": 0,
        "Cpuset": "",
        "Domainname": "",
        "Entrypoint": null,
        "Env": [
            "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
            "LC_ALL=en_US.UTF-8",
            "R_BASE_VERSION=3.1.2"
        ],
        "ExposedPorts": null,
        "Hostname": "03797203757d",
        "Image": "77b9aab5d3f0b345c921a19bf29f3bc10ecc3712d9b55f98d35404b001f8574a",
        "MacAddress": "",
        "Memory": 0,
        "MemorySwap": 0,
        "NetworkDisabled": false,
        "OnBuild": [],
        "OpenStdin": false,
        "PortSpecs": null,
        "StdinOnce": false,
        "Tty": false,
        "User": "",
        "Volumes": null,
        "WorkingDir": ""
    },
    "container": "ad8b63a987e194bf19b6eecdb2bfb39576c1952601e8165937ee97f2925b017e",
    "container_config": {
        "AttachStderr": false,
        "AttachStdin": false,
        "AttachStdout": false,
        "Cmd": [
            "/bin/sh",
            "-c",
            "#(nop) CMD [R]"
        ],
        "CpuShares": 0,
        "Cpuset": "",
        "Domainname": "",
        "Entrypoint": null,
        "Env": [
            "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
            "LC_ALL=en_US.UTF-8",
            "R_BASE_VERSION=3.1.2"
        ],
        "ExposedPorts": null,
        "Hostname": "03797203757d",
        "Image": "77b9aab5d3f0b345c921a19bf29f3bc10ecc3712d9b55f98d35404b001f8574a",
        "MacAddress": "",
        "Memory": 0,
        "MemorySwap": 0,
        "NetworkDisabled": false,
        "OnBuild": [],
        "OpenStdin": false,
        "PortSpecs": null,
        "StdinOnce": false,
        "Tty": false,
        "User": "",
        "Volumes": null,
        "WorkingDir": ""
    },
    "created": "2015-02-17T05:51:23.32446339Z",
    "docker_version": "1.5.0",
    "id": "0f9a4a6133e94d2e2ae092d447cfcc5366145ab62799de1c706ac9af90ce002a",
    "os": "linux",
    "parent": "77b9aab5d3f0b345c921a19bf29f3bc10ecc3712d9b55f98d35404b001f8574a"
}

$ sudo tree -L 2 Docker
Docker
├── aufs
│   ├── diff
│   ├── layers
│   └── mnt
├── containers
├── execdriver
│   └── native
├── graph
│   ├── 0e30e84e9513cb3d9d991389adfb77ac6afc9d75a5234e3d61af2f080c75d0ce
│   ├── 0f9a4a6133e94d2e2ae092d447cfcc5366145ab62799de1c706ac9af90ce002a
│   ├── 1f17c3b77bd72500adf49e5cfb9fcc78b004b9714ea7497031f8258bd95a51a0
│   ├── 326e7f15a5c9831976703bd25c84a02548c2dbec3514447f6d29b58e0fc4c6cf
│   ├── 511136ea3c5a64f264b78b5433614aec563103b4d4702f3ba7d4d2698e22c158
│   ├── 53e67b52fa37780ab20d519569cc734919d4b226e086b369b0472649d68825bd
│   ├── 5e8cefe0213ea6630ddfed346b255467ca35c22abc4b876bd4a2865dbe3a0a3f
│   ├── 77b9aab5d3f0b345c921a19bf29f3bc10ecc3712d9b55f98d35404b001f8574a
│   ├── 8771fbfe935cde12b40418e029cdb68adff76d740eddb72fc6c811b1b4c16a3e
│   ├── b00c2273d1a6ed96c88465612ea5e5ea1f1f10305151d2f9ddd94ec279d9e94f
│   ├── b608f23507fe1fbcb36641ff7ea21efa046fef3977ced56449c32e53d9bbe65d
│   ├── be55497bbb9c1aaa4fc18af5928217430f81fad8ca5a2dd420326f844f55b8d7
│   ├── e1a31145a2addc108cd77af268d3f4312b954081ddd7e3522026047a8f29b11f
│   └── _tmp
├── init
│   └── dockerinit-1.0.1
├── linkgraph.db
├── repositories-aufs
└── volumes

$ sudo ls -lh Docker/aufs/diff/8771fbfe935cde12b40418e029cdb68adff76d740eddb72fc6c811b1b4c16a3e/
total 76K
drwxr-xr-x  2 root root 4.0K Jan 27 11:55 bin
drwxr-xr-x  2 root root 4.0K Nov 30 07:37 boot
drwxr-xr-x  2 root root 4.0K Jan 27 11:56 dev
drwxr-xr-x 41 root root 4.0K Jan 27 11:55 etc
drwxr-xr-x  2 root root 4.0K Nov 30 07:37 home
drwxr-xr-x  9 root root 4.0K Nov 27 14:59 lib
drwxr-xr-x  2 root root 4.0K Jan 27 11:51 lib64
drwxr-xr-x  2 root root 4.0K Jan 27 11:49 media
drwxr-xr-x  2 root root 4.0K Jan 27 11:49 mnt
drwxr-xr-x  2 root root 4.0K Jan 27 11:49 opt
drwxr-xr-x  2 root root 4.0K Jan 27 11:56 proc
drwx------  2 root root 4.0K Jan 27 11:49 root
drwxr-xr-x  3 root root 4.0K Jan 27 11:49 run
drwxr-xr-x  2 root root 4.0K Jan 27 11:55 sbin
drwxr-xr-x  2 root root 4.0K Jan 27 11:49 srv
drwxr-xr-x  2 root root 4.0K Nov 11 14:37 sys
drwxrwxrwt  2 root root 4.0K Jan 27 11:56 tmp
drwxr-xr-x 10 root root 4.0K Jan 27 11:49 usr
drwxr-xr-x 11 root root 4.0K Jan 27 11:49 var
$ sudo ls -lh Docker/graph/8771fbfe935cde12b40418e029cdb68adff76d740eddb72fc6c811b1b4c16a3e/
total 8.0K
-rw------- 1 root root 1.6K Feb 22 16:19 json
-rw------- 1 root root    9 Feb 22 16:19 layersize

Monitor tools

cTop – A Command-Line Tool For Container Monitoring And Management In Linux, ctop

Docker Machine

Docker Machine is a tool that lets you

  • Install Docker Engine on virtual hosts. You can use Machine (a unified way) to create Docker hosts on your local Mac or Windows box, on your company network, in your data center, or on cloud providers like Azure, AWS, or Digital Ocean. See the comment on here.
  • Provision and manage multiple remote Docker hosts
  • Provision Swarm clusters

Docker machine is not installed in Linux when you install Docker. See the instruction on here to install it.

My feeling is if we just want to play Docker on a local Linux machine, we don't really need to use Docker Machine (it just make life more complicated). But if we are working on Mac/Windows or we want to work on clouds or test on VirtualBox, we shall use Docker machines.

Use Docker-machine to Create Docker Servers. Compare the Docker images on the local machine (server 1) & a new host (server 2) created by docker-machine. Question: 1. how to tell we are in the host/machine environment? 2. how to exit the host environment after we use eval $() command? docker-machine stop MachineName.

$ docker-machine help
$ docker-machine create --driver=virtualbox test
# Follow its hint on the output, issue the following command
$ docker-machine env test
# Follow its hint on the output, issue the following command
$ eval$(docker-machine env test) # will configure the docker CLI to connect to this docker machine 'test'
                                 # This is equivalent to running 4 export commands on the command line
$ docker-machine ls  # Very useful
$ docker-machine stop test
$ docker-machine ip test
$ docker-machine start test
$ docker-machine rm test

Play Docker Machine on Mac with Virtualbox. Docker can be used to create a virtual machine just like Vagrant.

$ docker-machine create -d virtualbox demo
$ docker-machine ls

# first way to access a Docker host
$ docker-machine ssh demo
docker@demo:~$ docker images # empty for now

# second way to access 
$ docker-machine env demo
$ eval $(docker-machine env demo)
$ docker version

RancherOS demo video used the docker-machine command to pull and run the RancherOS.

docker-machine create -d virtualbox --virtualbox-boot2docker-url https://releases.rancher.com/os/latest/rancheros.iso demo
docker-machine ssh demo
ps
docker ps
sudo system-docker ps

sudo ros help
sudo ros console list
sudo ros console switch ubunu
apt-get help

Docker Compose <docker-compose.yaml>

Docker Compose can help us out as it allows us to specify a single file in which we can define our entire environment structure and run it with a single command (much like a Vagrantfile works). Dockerfile vs docker-compose.yml

Docker Swarm

Moby Project

What is Docker's Moby Project?

Applications

Some popular Linux applications such as: owncloud, lamp, openstack, node.js, roundcube, DLNA/Server, madsonic, webproxy/webfilter, DHCP/DNS-Server like dnsmasq, cloudprint, ...

Dockerizing Compiled Software

https://ram.tianon.xyz/post/2017/12/26/dockerize-compiled-software.html

Illumina BaseSpace

Bioinformatics analyses

Cloud provider

Docker can be deployed on any cloud provider like Digital Ocean, Amazon Web Services (AWS), Microsoft Azure, Google Cloud Computing.

ownCloud

After I use docker run --rm --name myowncloud -p 81:80 owncloud:8.1, I find I can only access it through http://localhost:81. If I try to access it through another computer by http://xxx.xxx.xx.1:81, the URL is changed back to http://localhost:81 so it failed to load.

nextcloud

I feel nextcloud is a little modern than owncloud though their interface are very similar. I got the same problem (URL is changed from IP to localhost) when I try to access its web from another computer. Using the IP instead of localhost to finish the initial setup can fix the error.

Note:

  • Nextcloud uses owncloud mobile application.
  • Nextcloud includes a small mp4 file. I can use browser to play mp4. Photos files can be opened in browsers too (including slideshow).
  • The pdf file will be downloaded instead of opening on the browser. It can be easily fixed.
    • Click '+Apps' from the personal settings (the response is slow when I tested using Docker). Search for pdf viewer. Click the 'Enable' button (it will be changed to 'Disable' after that)
  • For mp3, no apps are shipped with nextcloud.
    • Audio Player. When I play mp3 files, the web interface does not show a progress bar:(
      $ docker run --rm --name mynextcloud -v ~/Downloads/nextcloudapps:/var/www/html/custom_apps -p 81:80 nextcloud
      # above will create an empty folder ~/Downloads/nextcloudapps (www-data:root)
      $ tar xzvf Downloads/audioplayer-2.3.1.tar.gz -C Downloads/
      $ docker cp Downloads/audioplayer mynextcloud:/var/www/html/custom_apps
      # Go to nextcloud and '+Apps', a new app 'Audio Player' should have shown up.
      
    • Music. GOOD. The app is from the owncloud team though for some reason the app is not included in owncloud/nextcloud. Yes, a progress bar is shown when I played a song downloaded from Youtube:)
      # No need to create a volume
      $ docker run --rm --name mycloud -p 81:80 nextcloud
      
      # Open another terminal
      # Don't download the zip file from github. Get the zip file from the app store
      $ tar xzvf ~/Downloads/music_0.7.0_nc-signed.tar.gz -C ~/Downloads/
      $ docker cp Downloads/music mynextcloud:/var/www/html/custom_apps
      $ docker exec mynextcloud chmod -R 0750 /var/www/html/custom_apps
      $ docker exec mynextcloud chown -R www-data:www-data /var/www/html/custom_apps
      

Use with R

$ docker run --net=host --rm -ti rocker/r-base
Unable to find image 'rocker/r-base:latest' locally
latest: Pulling from rocker/r-base
ae5da26d7cb2: Pull complete
2d9c896cd744: Pull complete
513d0440e189: Pull complete
e026193e1093: Pull complete
c8a303e77456: Pull complete
6df06abbd238: Pull complete
Digest: sha256:201df44988bf81b78adcc0fdc7d078a947ed56b6b264b9877f801eb9be3804c2
Status: Downloaded newer image for rocker/r-base:latest

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
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> q()
Save workspace image? [y/n/c]: n
$

Dockerfile

Create a new directory and a new file 'Dockerfile' with the content.

FROM debian:testing
MAINTAINER Dirk Eddelbuettel edd@debian.org
## Remain current
RUN apt-get update -qq
RUN apt-get dist-upgrade -y
RUN apt-get install -y --no-install-recommends r-base r-base-dev r-recommended littler
RUN ln -s /usr/share/doc/littler/examples/install.r /usr/local/bin/install.r

NOTE

  1. I ran into errors when I use the above (short) Dockerfile. But the Dockerfile from rocker (leave out the last line of launching R) works well. The R packages built in the image include 'docopt', 'magrittr', 'stringi', and 'stringr'.
  2. Install R package is possible when we launch a container. But we are not able to save the packages?? The rocker wiki also mentions something about installing packages.
  3. See also How to save data in wiki.

docker run

Note that if we are using the Dockerfile above to create an image, we will be dropped to the Linux shell. If we are pulling the rocker/r-base image from Docker Hub, we will be in R console directly. See the last line of Dockerfile on github website for rocker.

Then run the following to do some exercise (We could possibly replace 21b6a9e8b9e8 with your image ID or use rocker/r-base). For simplicity, we can try the colortools package first which does not depend on other packages and there is no need to compile the package.

sudo docker build -t debian:testing-add-r . # create an image based on the above Dockerfile
wget http://cran.r-project.org/src/contrib/sanitizers_0.1.0.tar.gz
sudo docker run -v `pwd`:/mytmp -t 21b6a9e8b9e8 \
     R CMD check --no-manual --no-build-vignettes /mytmp/sanitizers_0.1.0.tar.gz
sudo docker run -v `pwd`:/mytmp -t 21b6a9e8b9e8 \
     Rdevel CMD check --no-manual --no-build-vignettes /mytmp/sanitizers_0.1.0.tar.gz

sudo docker search eddelbuettel
sudo docker pull eddelbuettel/docker-ubuntu-r   # default tag is 'latest'; actually older than the other tags
sudo docker images eddelbuettel/docker-ubuntu-r # see the tag column
sudo docker pull eddelbuettel/docker-ubuntu-r:add-r # the tag name can only be obtained from hub.docker.com
sudo docker images eddelbuettel/docker-ubuntu-r # see the tag column
sudo docker pull eddelbuettel/docker-ubuntu-r:add-r-devel
sudo docker images eddelbuettel/docker-ubuntu-r # see the tag column
sudo docker run -v `pwd`:/mytmp -t 54d865dbd2c9 R CMD check --no-manual --no-build-vignettes /mytmp/sanitizers_0.1.0.tar.gz

sudo docker run -t -i eddelbuettel/docker-ubuntu-r /bin/bash
$ sudo docker images
REPOSITORY                     TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
debian                         testing-add-r       21b6a9e8b9e8        28 minutes ago      572.2 MB
ubuntu                         14.04               ed5a78b7b42b        4 days ago          188.3 MB
ubuntu                         latest              ed5a78b7b42b        4 days ago          188.3 MB
debian                         testing             88ba2870bfbe        7 weeks ago         154.7 MB
eddelbuettel/docker-ubuntu-r   add-r-devel         c998a74a1fb4        11 weeks ago        460.4 MB
eddelbuettel/docker-ubuntu-r   add-r               54d865dbd2c9        11 weeks ago        460.4 MB
eddelbuettel/docker-ubuntu-r   latest              a7cd5ddeb98e        5 months ago        515.4 MB

sudo docker logs xxxxx                # view the log
sudo docker restart xxxxx
sudo docker exec -it xxxx /bin/bash   # view any changes in R library
sudo docker stop xxxxx
sudo docker docker rm xxxxx

This is another example of using 'docker run' accompanying MotifBreakR package.

Testing R packages

Docker for R Package Development

http://www.jimhester.com/2017/10/13/docker/

A DevOps Perspective

More examples

R -> Docker

Docker for Shiny Server

# specify --name so we don't need to use container id to access it later
$ docker run -d --name rshiny -p 81:3838 rocker/shiny 

$ docker ps -l

# Run in container's bash
# https://stackoverflow.com/questions/30172605/how-to-get-into-a-docker-container
# non-interactive
$ docker exec -it rshiny ip addr  
1: lo: <LOOPBACK,UP,LOWER_UP> mtu 65536 qdisc noqueue state UNKNOWN group default qlen 1
    link/loopback 00:00:00:00:00:00 brd 00:00:00:00:00:00
    inet 127.0.0.1/8 scope host lo
       valid_lft forever preferred_lft forever
22: eth0@if23: <BROADCAST,MULTICAST,UP,LOWER_UP> mtu 1500 qdisc noqueue state UP group default 
    link/ether 02:42:ac:11:00:02 brd ff:ff:ff:ff:ff:ff link-netnsid 0
    inet 172.17.0.2/16 scope global eth0
       valid_lft forever preferred_lft forever

# interactive shell
$ docker exec -it rshiny bash 
root@5b78988d5619:/# who
root@5b78988d5619:/# which R
/usr/bin/R
root@5b78988d5619:/# ls /home
docker	shiny
root@5b78988d5619:/# ls /srv/shiny-server
01_hello  02_text  03_reactivity  04_mpg  05_sliders  06_tabsets  07_widgets  08_html  09_upload  10_download  11_timer  index.html  sample-apps
root@5b78988d5619:/# R -e 'package.Description("glmnet")'
root@5b78988d5619:/# exit

$ docker stop rshiny
$ docker rm rshiny   # remove the container

It is also useful to use the -v option in docker run so the local directory (eg /srv/shinyapps/) can be mapped to the docker volume (/srv/shiny-server).

# Put your shiny app in host's /srv/shinyapps/appdir,
$ docker run -d -p 81:3838 \
    -v /srv/shinyapps/:/srv/shiny-server/ \
    -v /srv/shinylog/:/var/log/shiny-server/ \
    rocker/shiny

And check running status

$ docker ps -a

Check opened ports

See What network ports are open: lsof or netstat.

$ netstat -ant
Active Internet connections (servers and established)
Proto Recv-Q Send-Q Local Address           Foreign Address         State      
tcp        0      0 0.0.0.0:22              0.0.0.0:*               LISTEN     
tcp        0      0 127.0.0.1:25            0.0.0.0:*               LISTEN     
...
tcp6       0      0 :::80                   :::*                    LISTEN     
tcp6       0      0 :::81                   :::*                    LISTEN     
tcp6       0      0 :::22                   :::*                    LISTEN     
tcp6       0      0 ::1:25                  :::*                    LISTEN

Docker containers for Bioconductor

The Dockerfiler for different images can be found on github.com/Bioconductor/bioc_docker.

Today is 2/5/2015.

$ sudo docker pull bioconductor/release_base
$ sudo docker images 
REPOSITORY                     TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
bioconductor/release_base      latest              7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150130            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150129            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150201            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150202            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150203            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150204            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150205            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150128            7eefbf783d9b        8 days ago          2.602 GB
bioconductor/release_base      20150131            7eefbf783d9b        8 days ago          2.602 GB

Note that even we specify the tag 'latest' we still get the same list of images as above

$ sudo docker pull bioconductor/release_base:latest

BiocImageBuilder

Reproducible Bioconductor workflows using browser-based interactive notebooks and containers

Nginx

httpd/apache

https://hub.docker.com/_/httpd/

MySQL

Deploying MySQL on Linux with Docker

Mail server

Setup Your Own Email Server with Docker

Mediawiki

$ ls -l ~/wiki_root
total 24
drwxr-xr-x 3 root     root     4096 Jul 10 10:09 data
drwxrwxr-x 3 brb      brb      4096 Jul 10 09:23 db
drwxrwxr-x 2 www-data www-data 4096 Jul 10 09:23 extensions
drwxrwxr-x 2 www-data www-data 4096 Jul 10 09:23 images
-rw-rw-r-- 1 www-data www-data 4152 Jul 10 11:12 LocalSettings.php
brb@galliumos:~$ tree mysql
mysql
├── conf.d
│   └── mysql.cnf
├── data
│   ├── auto.cnf
│   ├── ca-key.pem
│   ├── ca.pem
│   ├── client-cert.pem
│   ├── client-key.pem
│   ├── ib_buffer_pool
│   ├── ibdata1
│   ├── ib_logfile0
│   ├── ib_logfile1
│   ├── ibtmp1
│   ├── mediawiki [error opening dir]
│   ├── mysql [error opening dir]
│   ├── performance_schema [error opening dir]
│   ├── private_key.pem
│   ├── public_key.pem
│   ├── server-cert.pem
│   ├── server-key.pem
│   ├── sys [error opening dir]
│   └── wikidb [error opening dir]
├── dumps
└── initdb.d

9 directories, 15 files

brb@galliumos:~$ tree -L 2 mediawiki/
mediawiki/
├── config
│   └── LocalSettings.php
├── extensions
│   ├── Cite
│   ├── ConfirmEdit
│   ├── Gadgets
│   ├── ImageMap
│   ├── InputBox
│   ├── Interwiki
│   ├── LocalisationUpdate
│   ├── Nuke
│   ├── ParserFunctions
│   ├── PdfHandler
│   ├── Poem
│   ├── README
│   ├── Renameuser
│   ├── SpamBlacklist
│   ├── SyntaxHighlight_GeSHi
│   ├── TitleBlacklist
│   └── WikiEditor
└── images
    └── README

19 directories, 3 files

BookStack

BookStack is a simple, self-hosted, easy-to-use platform for organising and storing information.

https://github.com/solidnerd/docker-bookstack

Media server: Airsonic media server

https://airsonic.github.io/download/

Media server: Plex

Official Docker container for Plex Media Server

DNS server

Private DNS server container

ONLYOFFICE

NAS & Docker

http://www.ithome.com.tw/tech/96500

Some examples

  • GetLab專案管理工具
  • Jenkins開發版本管理工具

Run a benchmark program on ARM devices

Set up a Mastodon Instance on Linux

Your Own Social Network: How to Set Up a Mastodon Instance on Linux

Bioinformatics tools (Tophat, BWA, et al)

https://github.com/dceoy/docker-bio

GIVE - Genomic Interactive Visualization Engine

https://github.com/Zhong-Lab-UCSD/Genomic-Interactive-Visualization-Engine/blob/master/tutorials/GIVE-Docker.md

Elastic Search

Orchestrator

Kubernete

Kubernete vs Docker swarm

Other containers

Singularity

  • Singularity enables users to have full control of their environment; Singularity containers let users run applications in a Linux environment of their choosing. No 'sudo' is needed in general unless you want to build a container from a recipe.
  • Containers are more like an executable file for you to use
  • Containers are stored under the current location. It does not have a centre location (like /etc/default/docker.io if we use docker) to store images.
  • Can convert Docker containers to Singularity and run containers directly from Docker Hub
  • These bind points cannot be created unless the path already exists within the container. To ensure access to these storage spaces and remedy bind point errors, create these directories in the %post section of your Bootstrap file.
  • Singularity Hub

Ref:

Comparison of docker and singularity commands:

docker singularity
$ docker pull ubuntu:latest
$ docker pull broadinstitute/gatk3:3.8-0
$ singularity pull docker://ubuntu:latest
$ singularity pull docker://broadinstitute/gatk3:3.8-0
$ docker shell (not exist) $ singularity shell gatk3-3.8-0.img
> ls # the default location depends on the host system

> ls /usr # this is from the container

$ singularity shell --bind ~/Downloads:/mnt XXX.img
$ singularity shell docker://ubuntu:latest
# container is ephemeral

$ docker run --name test -it ubuntu date

# The next example is similar to 'singularity exec'
$ docker run --rm -i -t \
-v $(pwd):/usr/my_data \
broadinstitute/gatk3:3.8-0 \
bash /usr/my_data/myscript.sh
$ singularity run gatk3-3.8-0.img date
$ docker run --name ubuntu_bash --rm -i -t ubuntu bash
$ docker exec -d ubuntu_bash touch /tmp/execWorks
# Most useful
$ singularity exec gatk3-3.8-0.img java -version
$ singularity exec xxx.img cat /etc/*release

Shifter

Conda

Bioconda

Using docker to install conda (https://conda.io/docs/user-guide/tutorials/index.html)

$ docker run -t -i --name test --net=host ubuntu bash
# apt-get update
# apt-get install -y wget bzip2 python
# wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
# wget https://repo.continuum.io/archive/Anaconda2-5.1.0-Linux-x86_64.sh
# bash Miniconda2-latest-Linux-x86_64.sh
# bash Anaconda2-5.1.0-Linux-x86_64.sh
# exit

$ docker start test 
$ docker exec -i -t test bash
# conda list  # WORKS!
# conda config --add channels r
# conda config --add channels defaults
# conda config --add channels conda-forge
# conda config --add channels bioconda
# conda install bwa  (Segmentation fault. Core dumped)
# which bwa
/root/anaconda2/bin/bwa
# conda install r   (Only get 3.4.2 but the latest is 3.4.3.)
# conda install bowtie
# bowtie --version
# conda install gatk (https://bioconda.github.io/recipes/gatk/README.html)
   (Due to license restrictions, this recipe cannot distribute and install GATK directly)
   (R is downgraded to 3.2.2:( )
   (Segmentation fault. Core dumped)
# exit
# docker stop test
# docker rm test

Get miniconda image instead of using a Ubuntu image

$ docker pull continuumio/miniconda
$ docker run -i -t continuumio/miniconda /bin/bash
# conda install r   (get 3.4.2)
# conda config --add channels bioconda
# conda install bwa  (OK, no error)
# conda install gatk  (R was downgraded to 3.2.2, install openjdk 8.0.121)
# which gatk
/opt/conda/bin/gatk
# gatk -h
GATK jar file not found. Have you run "gatk-register"?

Issues:

  • R version is not up to date
  • So the problem is installing GATK requires an installation of R and the current R was affected.

CoreOS

Redhat has acquired CoreOS 1/31/2018.

Installation

We first boot a liveCD from any OS (CentOS works but Ubuntu 16.04 gave errors). In Virtualbox, we choose 'Red Hat' if we use CentOS.

Once the VM is created. We go to the settings. Create a bridged network or host-only network first (even we can get files from the host without creating a host-only network). Storage: choose CentOS-7.

  1. Get the install script from Github and create <coreos_install.sh> and chmod +x
  2. create <cloud-config.yaml> file which will include ssh_authorized_keys generated from another machine. It should also contain a new token for the cluster from https://discovery.etcd.io/new.
  3. ls -l /dev/sd*
  4. run sudo ./coreos_install.sh -d /dev/sda -C stable -c cloud-config.yaml. It will download the latest stable CoreOS, install to the HD
  5. Don't leave the VM or it will freeze. Issue sudo shutdown -h now once we see the word 'Success' at the last line of the output.
  6. Remove CentOS from the VM storage. Boot the coreOS VM.

The new screen shows corebm1 login with an IP. Go back to another machine and type ssh -i /tmp/CoreOSBM_rsa core@192.168.56.101. Inside CoreOS, we can type docker images.

The 'cloud-config.yaml file has to follow the format in https://coreos.com/os/docs/latest/cloud-config.html. Use the online validator https://coreos.com/validate/ to correct. At first I use the file from the youtube video. There is no error coming out when I ran the installation script. But I cannot connect to coreOS. The cloud-config.yaml file I use is (pay attention to '-', double quotes and indent characters)

#cloud-config
#
# set hostname
hostname: CoreBM1

# Set ssh key
ssh_authorized_keys:
  - "ssh-rsa AAAAB3 ..... brb@T3600"

coreos:
  etcd:
    discovery: "https://discovery.etcd.io/d3e95 .... "
# sudo ./installos -d /dev/sda -C stable -c cloud-config.yaml

CoreOS exploration

brb@T3600 /tmp $ ssh -i /tmp/id_rsa core@192.168.56.105
Enter passphrase for key '/tmp/id_rsa':
CoreOS stable (1010.6.0)
core@CoreBM1 ~ $
core@CoreBM1 ~ $ docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
core@CoreBM1 ~ $ df -h
Filesystem      Size  Used Avail Use% Mounted on
devtmpfs        1.4G     0  1.4G   0% /dev
tmpfs           1.4G     0  1.4G   0% /dev/shm
tmpfs           1.4G  340K  1.4G   1% /run
tmpfs           1.4G     0  1.4G   0% /sys/fs/cgroup
/dev/sda9        18G   23M   17G   1% /
/dev/sda3       985M  589M  345M  64% /usr
tmpfs           1.4G     0  1.4G   0% /media
/dev/sda1       128M   37M   92M  29% /boot
tmpfs           1.4G     0  1.4G   0% /tmp
/dev/sda6       108M   52K   99M   1% /usr/share/oem
core@CoreBM1 ~ $ free -m
             total       used       free     shared    buffers     cached
Mem:          2713        187       2525          0          9        109
-/+ buffers/cache:         68       2644
Swap:            0          0          0
core@CoreBM1 ~ $ lsb_release -a
-bash: lsb_release: command not found
core@CoreBM1 ~ $ docker pull ubuntu
Using default tag: latest
latest: Pulling from library/ubuntu
f069f1d21059: Pull complete
ecbeec5633cf: Pull complete
ea6f18256d63: Pull complete
54bde7b02897: Pull complete
Digest: sha256:bbfd93a02a8487edb60f20316ebc966ddc7aa123c2e609185450b96971020097
Status: Downloaded newer image for ubuntu:latest
core@CoreBM1 ~ $ docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
ubuntu              latest              0f192147631d        7 days ago          132.7 MB
core@CoreBM1 ~ $

CoreOS cluster discovery

https://coreos.com/os/docs/latest/cluster-discovery.html

etcd

fleet

Resource

Books

  • The Docker Book: Containerization is the new virtualization
  • Orchestrating Docker
  • Docker Hands on: Deploy, Administer Docker Platform

Blogs

Play with Docker (PWD)