Breakout Room 1: use BLAST from a container

Overview

Teaching: 0 min
Exercises: 20 min

Questions

Objectives

• Run a real-world bioinformatics application in a container

Goal

In this first breakout room, you’re going to lookup for a BLAST container image, download it, test it, and finally use it to run a quick blasting.
This example is adapted from the BioContainers documentation.

Before you start, cd into the appropriate directory:

cd /data/bio-intro-containers/exercises/blast_1

Search for a BLAST container image in a registry

Today you’re using the web registry RedHat Quay, at https://quay.io, to search the image we need. This registry contains all the images provided by the BioContainers project, so there are good chances of finding what you need here. The BioContainers home page, https://biocontainers.pro, also has a search function, however its user interface is a bit less friendly right now.

Now try and find the most recent container image for BLAST by BioContainers, using the Quay web site.

Solution

• Go to https://quay.io (NO registration required!);
• Locate the EXPLORE button on the top of the page, click on it, then in the search field type blast;
• We want an image from biocontainers, so look for biocontainers/blast and click on it;
• Click on the Tags icon on the left, and scroll the list of images to look for the highest Blast version, at the time of writing, it’s (2.10.1; among the multiple tags for this version, identify the most recent one;
• At the time of writing, the resulting image tag will be 2.10.1--pl526he19e7b1_2;
• You can click on the Fetch icon at the rightmost side of the record, select Pull by Tag, and then copy the full image name in your clipboard.
• At the time of writing, the full image specification is then quay.io/biocontainers/blast:2.10.1--pl526he19e7b1_2.

IMPORTANT: which image to use for the next steps?

As we don’t continuously update the content of this tutorial, please use the following image for the rest of this BLAST example:

quay.io/biocontainers/blast:2.9.0--pl526h3066fca_4

We’ve pre-cached this image in the virtual machine for this tutorial, so the following pull process should only take a few seconds.

Pull the container image for BLAST

To this end let’s use the appropriate singularity command.

Solution

singularity pull docker://quay.io/biocontainers/blast:2.9.0--pl526h3066fca_4

At the end an image SIF file for BLAST is downloaded:

ls blast*

blast_2.9.0--pl526h3066fca_4.sif

Run a test command

Now run a simple command using the image you just pulled, for instance blastp -help, to verify that it actually works.

Solution

singularity exec blast_2.9.0--pl526h3066fca_4.sif blastp -help

USAGE
  blastp [-h] [-help] [-import_search_strategy filename]

[..]

 -use_sw_tback
   Compute locally optimal Smith-Waterman alignments?

Now, the demo directory exercises/blast_1 contains a human prion FASTA sequence, P04156.fasta, as well as a gzipped reference database to blast against, zebrafish.1.protein.faa.gz. Let us uncompress the database first:

gunzip zebrafish.1.protein.faa.gz

Prepare the database

You now need to prepare the zebrafish database with makeblastdb for the search, using the following command through a container:

makeblastdb -in zebrafish.1.protein.faa -dbtype prot

Try and run it via Singularity.

Solution

singularity exec blast_2.9.0--pl526h3066fca_4.sif makeblastdb -in zebrafish.1.protein.faa -dbtype prot

Building a new DB, current time: 11/16/2019 19:14:43
New DB name:   /data/bio-intro-containers/exercises/blast_1/zebrafish.1.protein.faa
New DB title:  zebrafish.1.protein.faa
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 52951 sequences in 1.34541 seconds.

After the container has terminated, you should see several new files in the current directory (try ls).
Now let’s proceed to the final alignment step using blastp.

Run the alignment

Adapt the following command to run into the container:

blastp -query P04156.fasta -db zebrafish.1.protein.faa -out results.txt

Solution

singularity exec blast_2.9.0--pl526h3066fca_4.sif blastp -query P04156.fasta -db zebrafish.1.protein.faa -out results.txt

The final results are stored in results.txt:

less results.txt

                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

  XP_017207509.1 protein piccolo isoform X2 [Danio rerio]             43.9    2e-04
  XP_017207511.1 mucin-16 isoform X4 [Danio rerio]                    43.9    2e-04
  XP_021323434.1 protein piccolo isoform X5 [Danio rerio]             43.5    3e-04
  XP_017207510.1 protein piccolo isoform X3 [Danio rerio]             43.5    3e-04
  XP_021323433.1 protein piccolo isoform X1 [Danio rerio]             43.5    3e-04
  XP_009291733.1 protein piccolo isoform X1 [Danio rerio]             43.5    3e-04
  NP_001268391.1 chromodomain-helicase-DNA-binding protein 2 [Dan...  35.8    0.072
[..]

When you’re done, quit the view by hitting the q button.

Well done, you’ve just BLASTed a sequence using a container!

Key Points

• Lookup for containers in online image registries

• Download container images with singularity pull

• Perform a simple test to check the application works, e.g. request the help output

• Run application commands in a container by prepending with singularity exec <image>