Docker: Difference between revisions
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= Applications = | = Applications = | ||
Some popular Linux applications such as: owncloud, lamp, openstack, node.js, roundcube, DLNA/Server, madsonic, webproxy/webfilter, DHCP/DNS-Server like dnsmasq, cloudprint, ... | |||
== Illumina BaseSpace == | == Illumina BaseSpace == | ||
* http://blog.basespace.illumina.com/2013/10/21/introducing-the-native-app-engine/ | * http://blog.basespace.illumina.com/2013/10/21/introducing-the-native-app-engine/ | ||
Revision as of 23:08, 17 February 2015
Official web page http://docker.io
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.
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.
Usage
Basics, docs, cheatsheet
- https://docs.docker.com/articles/basics/
- https://coderwall.com/p/2es5jw/docker-cheat-sheet-with-examples
- https://github.com/wsargent/docker-cheat-sheet
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:/#
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
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.
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
Viewing our Web Application Container
$ sudo docker ps -l $ sudo docker run -d -p 5000:5000 training/webapp python app.py
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
Restart a Container
$ sudo docker start nostalgic_morse OR $ sudo docker restart nostalgic_morse
Removing our Web Application Container
$ sudo docker stop nostalgic_morse $ sudo docker rm nostalgic_morse
Note: Always remember that deleting a container is final!
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)
It is also helpful to create bash aliases for these commands by editing ~/.bash_aliases file.
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
Dockerfile
hub.docker.com
- Note that Dockerfile is optional on https://registry.hub.docker.com.
- rocker. The dockerfile is included there.
- Search all repositories related to R
- baseimage-docker. I can use ping command without special argument when I start phusion/baseimage.
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).
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
Access the internet from the container
Run the container with the '--net=host' option
sudo docker run --net=host -it ubuntu /bin/bash
Applications
Some popular Linux applications such as: owncloud, lamp, openstack, node.js, roundcube, DLNA/Server, madsonic, webproxy/webfilter, DHCP/DNS-Server like dnsmasq, cloudprint, ...
Illumina BaseSpace
- http://blog.basespace.illumina.com/2013/10/21/introducing-the-native-app-engine/
- https://developer.basespace.illumina.com/docs/content/documentation/getting-started/overview
- https://developer.basespace.illumina.com/docs/content/documentation/native-apps/manage-docker-image
Use with R
- http://dirk.eddelbuettel.com/papers/useR2014_keynote.pdf and http://dirk.eddelbuettel.com/papers/r_and_docker_sep2014.pdf
- http://dirk.eddelbuettel.com/blog/2014/10/23/
- Running RStudio and the instruction using rocker.
- Rocker
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
Docker containers for Bioconductor
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
Resource
Books
- The Docker Book: Containerization is the new virtualization
- Orchestrating Docker
- Docker Hands on: Deploy, Administer Docker Platform