Revision as of 11:21, 4 February 2015

Installation

Ubuntu

https://docs.docker.com/installation/ubuntulinux

Windows

Note: Docker has been tested on Windows 7.1 and 8; it may also run on older versions. 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 virtual 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 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.

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:/#

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

Dockerizing Applications

$ sudo docker run -d 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.

Web Application/Work with containers

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

$ sudo docker run -d -P training/webapp python app.py
$ sudo docker run -d -p 5000:5000 training/webapp python app.py
$ sudo docker ps   # find the NAME from the last column
                   # In this case, it is called 'nostalgic_morse'
$ sudo docker port nostalgic_morse 5000
$ sudo docker logs -f nostalgic_morse
$ sudo docker top nostalgic_morse
$ sudo docker stop nostalgic_morse
$ sudo docker ps -l
$ sudo docker start nostalgic_morse
$ sudo docker stop nostalgic_morse
$ sudo docker rm nostalgic_morse

Note: Always remember that deleting a container is final!

Work with container images

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

$ 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 <[email protected]>
 ---> 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

hub.docker.com

rocker

Link containers together

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

Manage data in containers

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

Working with Docker hub

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

Misc

Vagrant vs Docker

http://stackoverflow.com/questions/16647069/should-i-use-vagrant-or-docker-io-for-creating-an-isolated-environment

Access the internet from the container

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

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

Applications

Illumina BaseSpace

Use with R

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

FROM debian:testing
MAINTAINER Dirk Eddelbuettel [email protected]
## 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

Then run the following to do some exercise.

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

@@ Line 515: / Line 515: @@
 eddelbuettel/docker-ubuntu-r   latest              a7cd5ddeb98e        5 months ago        515.4 MB
 </pre>
+== [http://www.bioconductor.org/help/docker/ Docker containers for Bioconductor] ==

Docker: Difference between revisions

Revision as of 11:21, 4 February 2015

Contents

Installation

Ubuntu

Windows

Increase boot2docker vmdk space

Install utilities in Boot2docker VM

Mac

Usage

Basics, docs, cheatsheet

A brief intro to docker virtualization

Dockerizing Applications

Web Application/Work with containers

Work with container images

hub.docker.com

Link containers together

Manage data in containers

Working with Docker hub

Misc

Vagrant vs Docker

Access the internet from the container

Applications

Illumina BaseSpace

Use with R

Docker containers for Bioconductor

Navigation menu

Docker: Difference between revisions

Revision as of 11:21, 4 February 2015

Installation

Ubuntu

Windows

Increase boot2docker vmdk space

Install utilities in Boot2docker VM

Mac

Usage

Basics, docs, cheatsheet

A brief intro to docker virtualization

Dockerizing Applications

Web Application/Work with containers

Work with container images

hub.docker.com

Link containers together

Manage data in containers

Working with Docker hub

Misc

Vagrant vs Docker

Access the internet from the container

Applications

Illumina BaseSpace

Use with R

Docker containers for Bioconductor

Navigation menu

Search