Docker hands-on workshop at UC Davis

Dr. C. Titus BrownDocker hands-on workshop at UC Davis

Lots of workshops available at UCD, open to everyone and free! (sign up, as max capacity is 40) Entry and intermediate levels available. Data Science Initiative is a hub for data science on campus with space available for workshops in the library at UC Davis, which is where we are located today! All materials are CC0, feel free to re-package and use for your own purposes and workshops.

Check out training organizations, Data Carpentry and Software Carpentry programming software development and data science, short two-day local workshops available internationally, beginner to intermediate skills.

Also available: Michael Barton from DOE-JGI lead on bioboxes and nucleotid.es

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Materials for today:

https://github.com/ngs-docs/2015-nov-docker

Intro:

https://github.com/ngs-docs/2015-nov-docker/blob/master/docker-intro.rst

Launch EC2 m3.xlarge instance (15 GB RAM, 4 cores and 2×40 SSD, renting around $0.12/hr), install stuff. Log out, log back in.

Docker containers are lightweight, can grow and shrink in ways VMs cannot. Access-level sandbox. Philosophy of community-level and light-weight is appealing in the sense that it’s accessible.

docker
Need host environment. Docker runs natively on linux os. We’ll use AWS to install Docker. Almost all workshops available through dib lab are via AWS, minimizes problems dealing with local hardware. Instructions here.

Ubuntu 14.04 LTS, downstream of Debian, Long-term Support (LTS) for 5 years (until 2019). So, all materials here should be stable until then.

Get it all working first by copy-pasting commands directly from tutorial. (You’ll learn less this passive way, but then make sure to go back later and change things up to see what happens. This will increase understanding.)

Main idea is that you need to download and run Docker as root. (Exceptionally bad idea to do, in general! We’re assuming we can trust Docker at this point, but usually we encourage to be more skeptical of downloading things from websites and running as root.) Need root privileges. (Some HPC systems will not grant users root privaleges. Docker cannot be run in this case.) Nice thing about AWS is if you screw something up, running as root, we’re deleting the instance anyway. Get docker running, prompt will change (this is bash prompt inside Docker container, mostly isolated from host operating system):

rundocker

Host accommodates many Docker containers, which each have their own file systems. Uses host hardware. Dependent on the size of the machine. If you have Mac/Windows configured with Linux VM, then the Docker will be dependent on the hardware designated for the VM. Docker Machine allows a backend memory allocation. Everything you did in the Docker, when you exit, Docker is deleted. It’s accessible again only if you know what your’e looking for. New fresh Docker container starts each time. If you want to spin up Docker containers all running web server, Docker is awesome for that. For bioinformatics workflows, not main customer base for Docker, this is not well worked out, much less supported with little infrastructure existing. Titus’ idea is to scale out, move computing to data rather than move data to computing. With Docker containers, can spinning up software processing >1 TB datasets (don’t use shared file systems), using many EBS volumes, many EC2 instances. You could feasibly install and run individual software programs in separate Docker containers, e.g. trimmomatic (java) and megahit (assembly) which might have incompatibilities and periodic updates.

docker

Get data and put on host, not on Docker (since you want to run the Docker on the data. Bring the computing to the data, rather than the other way around). Then, run the docker container, run the assembly program command from within the container, exit. And the resulting data from the assembly after it’s finished are on the host!!!! SUPER COOL!!!! 🙂

megahit_docker

Actually, you can run this all piped into one command, without having to run the docker command separately from the program command.

docker run -v /home/ubuntu/data:/mydata \
   -it megahit_ctr \
sh -c '/home/megahit/megahit --12 /mydata/*.pe.fq.gz
                     -r /mydata/*.se.fq.gz
                     -o /mydata/ecoli -t 4'

Or, you can write a bash shell script (see tutorial), then run the script.

Create Dockerfile, which can be version controlled. When encoding the commands in a Dockerfile, each RUN command is a layer of the Dockerfile. Try to include as many commands in one RUN command as possible, to create less layers. None of this has to be repeated, once the Dockerfile has been created and pushed to the Docker hub (docker login, docker build -t titus/megahit ., and docker push titus/megahit). All you have to do is get the Dockerfile, install Dockerfile, know where your data are, and run!!!

Do challenge exercises:

https://github.com/ngs-docs/2015-nov-docker/blob/master/challenge-exercises.rst

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About Lisa Cohen

PhD student at UC Davis.
This entry was posted in Bioinformatics, workshops. Bookmark the permalink.

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