Docker image for VirMet

Docker containers are a lightweight alternative to virtual machines (VMs). We prepared an image pre-built with all necessary dependencies that can be downloaded and run with little effort. Docker runs on Linux, Windows and Mac OS X. Within any of these hosts, it will run an isolated container inside which VirMet is installed together with its dependencies. Make sure you have enough disk space (hundreds of gigabytes) to save databases.

Install docker

Follow the instructions reported here to install docker on your host machine.

Check your installation with docker version and docker run hello-world.

Pull docker image for VirMet

Simply type docker pull ozagordi/virmet. This will download approximately 1GB of data: it contains a Linux Ubuntu distribution with all the required software pre-installed.

Start a docker container

The command to give is the following (backslashes can be omitted if the command is given on a single line)

[user@host ~ ]$ docker run -it --name my_virmet \
-v your_path_to_some_data:/home/ubuntu/miseq_runs \
ozagordi/virmet /bin/bash

Let's see this command in detail.

The above command will drop you in a bash shell (/bin/bash) in a new container derived from the image ozagordi/virmet. This contained will be named my_virmet (you can choose the name you prefer) in interactive mode (-it), and it will mount a volume found on your host. Let's see an example of how we can use this mount option.

Substitute your_path_to_some_data to a global path where you are storing sequencing data. For example, if you have Miseq runs in /data/MiSeqOutput

[user@host ~ ]$ ls -1 /data/MiSeqOutput

then use the option -v /data/MiSeqOutput:/home/ubuntu/miseq_runs. What comes before the : is the global path on your host machine to the Miseq runs; this will be found inside the container at the path /home/ubuntu/miseq_runs. This is a convenient way to make data on your host machine available to the container, i.e. to VirMet.

The official reference for docker run is here.

Once in the container

The prompt is now different, now we are root inside the container (identified with an ID string) and the prompt reads root@18ef5268a7a4:/home/ubuntu#.

First of all one has to activate the conda environment with the correct installation of Python, pandas and Biopython. The command is

root@18ef5268a7a4:/home/ubuntu# source activate test-virmet

We can check that the host directory is correctly mounted

root@18ef5268a7a4:/home/ubuntu# ls /home/ubuntu/miseq_runs/

Good! The data directories on our host are mounted inside the container. Let's now make a directory to store our results

root@18ef5268a7a4:/home/ubuntu# mkdir results
root@18ef5268a7a4:/home/ubuntu# cd results

The first time we need to fetch (download) and index all databases, see the relevant instructions.

Once the databases are ready, we can finally run our first wolfpack command.

root@18ef5268a7a4:/home/ubuntu/results# virmet wolfpack --run /home/ubuntu/miseq_runs/160719_M01274_0159_000000000-AMA6L &

and wait for the results to appear.

Some suggestions

Mount multiple volumes

The -v option of docker run allows mounting of multiple volumes. For example one could mount the directory with sequencing data, one to store results and one for the databases by repeating -v multiple times

[user@host ~ ]$ docker run -it --name my_virmet \
-v your_path_to_some_data:/home/ubuntu/miseq_runs \
-v your_path_to_db:/data/virmet_databases \
-v your_path_to_results:/home/ubuntu/results \
ozagordi/virmet /bin/bash

This is convenient if one wants to have available all files both within the container and outside of it. In alternative, one can copy files from the container to the host with docker cp, see reference. Users are encouraged to get familiar with Docker and find the strategy that suits them best.

Leaving a container and attaching it again

A container can be left with ctrl + p, ctrl + q (release ctrl in between) and attached later with docker attach my_virmet (or any other name). It might be necessary to give an extra press to return. If we give ctrl + d inside the container this is left and stopped, so one has to start it again with docker start my_virmet before attaching it.