The goal of this tutorial is to show you the basics of building images using Docker.
For Linux users, you need to install [Docker engine] (https://docs.docker.com/engine/installation/). For PC and Mac users you need to install Docker toolbox for Mac and Windows and use [Docker Machine] (https://docs.docker.com/machine/get-started/) to create a virtual machine to run your Docker containers. Video series on setting up Docker on your machine: Mac, Windows and Linux. Recently Mac and Windows users can install Docker directly onto your computer without having to use virtual machines. Download Docker for Mac and Docker for Windows.
Dockerfile is a file that constains set of instructions/commands that are used to build the Docker image. Create a file called Dockerfile before building an image
mkdir ~/make_megahit
cd ~/make_megahit
cat <<EOF > Dockerfile
FROM ubuntu:14.04
RUN apt-get update
RUN apt-get install -y g++ make git zlib1g-dev python
RUN git clone https://github.com/voutcn/megahit.git /home/megahit \
&& cd /home/megahit \
&& git checkout 01b6692a4286973343da133f63d9e3c1252a5e8e \
&& make
ENTRYPOINT ["/home/megahit/megahit"]
EOF
Let's look at this Dockerfile before running it:
cat Dockerfile
Now see what each command in Docker file does::
The FROM command tells Docker what base image to load; the RUN commands tell Docker what to execute (and then save the results from);
and the ENTRYPOINT specifies the script entry point - a command that is run if no other command is given.
Let's build a Docker image from the above Dockerfile:
docker build -t megahit .
(This will take a few minutes..)
This creates a new image named megahit. If you run:
docker images
you should see something like:
REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE
megahit latest 749fd74397ed 29 seconds ago 427.5 MB
ubuntu 14.04 91e54dfb1179 3 days ago 188.4 MB
-------
-------
Once it's built, you can now test the built megahit image by running it like so ::
docker run megahit
You should see all the command line arguments for megahit image
But this is not so useful. You should test the same image using input arguments:
First download the test data into a scratch directory like so:
mkdir ~/my-scratch-dir
cd ~/my-scratch-dir
wget http://public.ged.msu.edu.s3.amazonaws.com/ecoli_ref-5m-trim.se.fq.gz
wget http://public.ged.msu.edu.s3.amazonaws.com/ecoli_ref-5m-trim.pe.fq.gz
And run the built image like so:
docker run -v ~/my-scratch-dir:/working-dir -w /working-dir \
megahit --12 ecoli_ref-5m-trim.pe.fq.gz \
-r ecoli_ref-5m-trim.se.fq.gz -o ecoli -t 4
If the tool's container produced outputs in that host's scratch directory (ecoli in this case), then your tool is working.
You can tag the image like so:
docker tag ubuntu/megahit:<tag> <user>/megahit:<tag>
If you wanted to make this broadly available, the next steps
would be to log into the [Docker Hub] (https://hub.docker.com/) and push it; I did so with these commands: docker login and docker push <user>/megahit:<tag>.
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Docker provides a nice way to bundle multiple packages of software together, for both yourself and for others to run.
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Docker gives you a good way to isolate what you're running from the data you're running it on.
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The Dockerfile enhances reproducibility by giving explicit instructions for what to install, rather than simply bundling it all in a binary.
Let's create a Dockerfile and image for SPAdes-3.5.0 assembler