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Docker Continuous Integration

This is a Docker automated build tutorial

Build on Docker Hub

  1. Go to Github and sign in if you already have an account or sign up if not.
  2. Create a new github repo and name it bowtie2-test
  3. In the bowtie2-test repo, create a new file, name it Dockerfile and fill it with the following:
FROM ubuntu:14.04 
RUN apt-get update -qq --fix-missing; \ 
	apt-get install -qq -y wget unzip; 
RUN wget -q -O bowtie2.zip http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.4/bowtie2-2.2.4-linux-x86_64.zip/download; \ 
	unzip bowtie2.zip -d /opt/; \ 
	ln -s /opt/bowtie2-2.2.4/ /opt/bowtie2; \ 
	rm bowtie2.zip 
ENV PATH $PATH:/opt/bowtie2
  1. Now go to Docker hub, link your Docker hub account to your bowtie2-test git repo
  2. In the build settings tab, trigger a new build, then keep an eye on the Build details tab
  3. Once the build is done, check the build details. If successful, make sure that the Dockerfile contents are copied in the Dockerfile tab
  4. Go to settings tab, and make the repo public
  5. Go to your VM and run docker search <your-docker-id> and you get an output like this:
NAME                             DESCRIPTION                         STARS           OFFICIAL            AUTOMATED
usit/bowtie2                     bowtie2 test                        0                                   [OK]
  1. Now test your bowtie2 image. run docker run --rm <your-docker-id>/bowtie2 bowtie2 --version
Unable to find image '<your-docker-id>/bowtie2-test:latest' locally
latest: Pulling from <your-docker-id>/bowtie2-test
c954d15f947c: Already exists
c3688624ef2b: Already exists
848fe4263b3b: Already exists
23b4459d3b04: Already exists
36ab3b56c8f1: Already exists
2025c15309ef: Pull complete
b7bbb25b5ed0: Pull complete
Digest: sha256:ef7a5e9df7e76ea294a6bd999393fca747d4b41e7f4b08a51c18d8bb4f273c71
Status: Downloaded newer image for <your-docker-id>/bowtie2-test:latest
/opt/bowtie2/bowtie2-align-s version 2.2.4
64-bit
Built on localhost.localdomain
Wed Oct 22 12:35:49 EDT 2014
Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-54)
Options: -O3 -m64 -msse2  -funroll-loops -g3 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Automated build

  1. Go to your bowtie2-test github repo and modify the Dockerfile (upgrading the bowtie2 version to 2.3.4):
FROM ubuntu:14.04 
RUN apt-get update -qq --fix-missing; \ 
	apt-get install -qq -y wget unzip; 
RUN wget -q -O bowtie2.zip http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4/bowtie2-2.3.4-linux-x86_64.zip/download; \ 
	unzip bowtie2.zip -d /opt/; \ 
	ln -s /opt/bowtie2-2.3.4-linux-x86_64/ /opt/bowtie2; \ 
	rm bowtie2.zip 
ENV PATH $PATH:/opt/bowtie2
  1. Now go to your docker hub repo, the Build details tab, and notice that a new build has been triggered
  2. After the build is completed, go to your VM and again run docker run --rm <your-docker-id>/bowtie2-test bowtie2 --version
Unable to find image '<your-docker-id>/bowtie2-test:2.3.4' locally
2.2.4: Pulling from <your-docker-id>/bowtie2-test
c954d15f947c: Already exists
c3688624ef2b: Already exists
848fe4263b3b: Already exists
23b4459d3b04: Already exists
36ab3b56c8f1: Already exists
c3a5acaf53e8: Pull complete
09c4c210758b: Pull complete
Digest: sha256:11c1615911d570cd55eea38f3a1e894a977a1b6efd599fdb4d71b89a3fa5f075
Status: Downloaded newer image for <your-docker-id>/bowtie2-test:2.3.4
/opt/bowtie2/bowtie2-align-s version 2.3.4.1
64-bit
Built on 14231912a8bd
Sat Feb  3 13:04:04 UTC 2018
Compiler: gcc version 4.8.2 20140120 (Red Hat 4.8.2-15) (GCC)
Options: -O3 -m64 -msse2 -funroll-loops -g3 -g -O2 -fvisibility=hidden -I/hbb_exe/include  -std=c++98 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Notice that only the two upper layers were pulled, while the other layers already existed

Multiple tags

  • create another branch on the github repo, e.g. 2.3.3, and modify the Dockerfile accordingly
  • In the Docker hub page, configure another build with the newly created branch and trigger it
  • On your VM, run docker pull -a <your-docker-id>/bowtie2-test and notice that two images with two tags are pulled

Privacy

  • In the Docker hub page, make <your-docker-id>/bowtie2-test private
  • Now on your VM, try to search for this repo. Not there, right? Now try to pull the image again
$ docker pull -a <your-docker-id>/bowtie2-test
Using default tag: latest
Error response from daemon: pull access denied for <your-docker-id>/bowtie2-test, repository does not exist or may require 'docker login
  • It is now private, and requires login. Now login and try again
$docker login
Login with your Docker ID to push and pull images from Docker Hub. If you don't have a Docker ID, head over to https://hub.docker.com to create one.
Username: <your-docker-id>
Password: <your-password>
Login Succeeded

$docker pull <your-docker-id>/bowtie2-test
Using default tag: latest
latest: Pulling from <your-docker-id>/bowtie2-test
c954d15f947c: Already exists
c3688624ef2b: Already exists
848fe4263b3b: Already exists
23b4459d3b04: Already exists
36ab3b56c8f1: Already exists
f481c2f4b7bc: Pull complete
b99a74a85307: Pull complete
Digest: sha256:45f58aecfe190eb57883e56a60e41c0a6c075e32ee13d82cba018e1481b8339a
Status: Downloaded newer image for <your-docker-id>/bowtie2-test:latest
  • Also notice that the repo is now not searchable on the Docker hub website

Add Collaborators

  • If you add a collaborator (another docker account) to a private repo, the repo will be visible to that account. Try this out!