Getting started with Rbbt

Overview

Rbbt stands for Ruby Bioinformatics Toolkit and as such can be seen as a collection of tools to perform bioinformatics. These basic building blocks of Rbbt are found in Ruby gems and they include code for things like gather data resources and create databases and indices to query them, create and enact workflows, or export functionalities through HTTP and REST. These ruby gems are the rbbt core system and are very simple to install.

Code is just one side of the coin in bioinformatics or any other data-intensive field, the other is of course data. Beyond the basic task implemented in the Rbbt core system are what we can call functionalities, this very general term is used to refer to anything from a lengthy analysis to a query system answering questions in real time. Bioinformatics functionalities typically require auxiliary datasets (such as files with basic genomic information) and some level of infrastructure (indices to query them). Rbbt implements a resource management system that will take care of gathering the data you need (or even third party software) and preparing it for use. This means that while this process will take require no action on the part of the user it might lead to a significant delay when an infrastructure is first use. Producing this infrastructure is what we call bootstrapping, and is the most important part getting Rbbt ready for use.

In Rbbt functionalities are packaged in what we call workflows, which include the code to bootstrap the infrastructure and the pipelines of analysis that implement these functionalities. Rbbt offers access to these functionalities via the command-line, programmatically, through REST web services, and through HTML templates. This scheme help us reuse and re-purpose functionalities and analytical pipelines in Rbbt often involve may workflows, specially when implementing omics analysis. Additionally the Workflows can override the boilerplate templates used to offer access to the functionalities via HTML to build incrementally more complex user interfaces.

Because bootstrapping and infrastructure might be very expensive, or require data that is not made available publicly, in Rbbt we often provide remote access to some functionalities. In Rbbt you can specify which workflows you want to use remotely and all your analytical pipeline will transparently relay that work to them, thus avoiding the use of any local infrastructure for those functionalities.

Installation

The first step in an Rbbt installation is to install the base system and the Ruby gems. This basically just means having Ruby installed and the Rbbt gems. However to fully use Rbbt a there are a few details that need to be worked out. The rbbt-image gem provides a convenient tool to produce provision files for docker images and virtual machines that will install the base system.

Follow the instructions in the install section.

Usage

The rbbt command

After the installation steps above we are ready to use rbbt. The main way to interact with the system is via de command rbbt which offers a convenient way to access many different tools. Its use is similar to other commands like git and follows the general syntax rbbt command subcommand1 subcommand2 --boolean_flag --option_key option_value arg1 arg2. As you time commands it will show you the subcommands available, and you can always use the --help or -h flag to get help on the available options.

The tools available include examining TSV files, monitoring the system status, configuring remote workflows, initiating web servers, and most importantly enacting workflow tasks. Lets look a that in more detail.

Workflow enactment in Rbbt

The most basic way to enact a workflow task is using the rbbt command as follows rbbt workflow task <workflow> <task> <options> for example, to translate the gene symbol TP53 to Ensembl ID you would run the following command (see the following sub-section before trying it out!):

rbbt workflow task Translation translate --genes TP53 --format "Ensembl Gene ID"

This command will output through STDOUT the code ENSG00000141510, as well some logs via the STDERR. To get more help on this command you can type rbbt workflow task Translation translate -h to see the available options¹ and even some examples.

Using a remote workflow

Running the command above would started the gathering of certain data files fomr the Ensembl BioMart and creating some indices to access them, i.e. bootstrapping some of the Translation workflow infrastructure. Queries to the Ensembl BioMart take a little while and you would end up probably interrupting the process and with a bad feeling about it. Instead let us first try to run the same command on one of the workflow servers maintained at CNIO.

rbbt workflow task https://rbbt.bsc.es/Translation translate --genes TP53 --format "Ensembl Gene ID"

Result

ENSG00000141510

Alternatively you can also configure the Translation workflow to always use that remote sever so that you can just write Translation

rbbt workflow remote add Translation https://rbbt.bsc.es/Translation

If you would like to install the infrastructure locally you can remove the remote server (if you created it)

rbbt workflow remote remove Translation

install the workflow locally (the code)

rbbt workflow install Translation

or alternative do export RBBT_WORKFLOW_AUTOINSTALL=true to have workflows autoinstall as needed. And run the command as initially, though in this case with a more verbose log level so you can monitor the process

rbbt workflow task Translation translate --genes TP53 --format "Ensembl Gene ID" --log 0

What next?

You have now gotten started with Rbbt. The next thing you can do is find interesting workflows you might want to check out at https://github.com/Rbbt-Workflows, or think of writing your own.