BioContainers in Examples

In this section we provide a set of examples about how to use BioContainers in your analysis. Please feel free to contribute to this help with your own examples.

Peptide MS search engine (Tide)

Let’s run a proteomics search engine to identified proteins using Tide. Proteomics data analysis is dominated by database-based search engines strategies. Amount Search Engines, Tide is one of the most popular nowadays.

Get the docker container

Note

The BioContainers community had decided to remove the latest tag. Then, the following command docker pull biocontainers/crux will fail. Read more about this decision in Getting started with Docker

Getting the data

First thing to do is to arrange the necessary. For this pipeline we need some mass spectrometry data and a protein database in FASTA format. This are the files we are using for this tutorial:

I’m placing all these files inside a folder in your machine, in my case I will use /Users/yperez/workspace/

Start searching

Note

To have access to files inside the container, and vice-versa, we need to map a local (/Users/yperez/workplace) folder inside the container (/data/). This is possible using the -v and passing the complete path from our folder that we wish to map inside the container.

After running this command you will see a new folder called yeast-index in your path (/Users/yperez/workplace).

If everything went well you should see two new folder (crux-output) containing the result files.

Command Resume

So far, you launched your first containers using the docker run command. You ran an interactive container that ran in the foreground. You also ran a detached container that ran in the background. In the process you learned about several Docker commands:

  • docker run - Run a docker container
  • dcoker pull - Download the container from Biodocker Hub
  • docker ps - Lists containers.
  • docker logs - Shows us the standard output of a container.
  • docker stop - Stops running containers.

Now, you have the basis learn more about Docker Go to “Run a simple application“