BioContainers Collection

Link to section 'What is BioContainers?' of 'BioContainers Collection' What is BioContainers?

The BioContainers project came from the idea of using the containers-based technologies such as Docker or rkt for bioinformatics software. Having a common and controllable environment for running software could help to deal with some of the current problems during software development and distribution. BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics containers with a special focus on omics fields such as proteomics, genomics, transcriptomics and metabolomics. . For more information, please visit BioContainers project.

Link to section ' Getting Started ' of 'BioContainers Collection' Getting Started

Users can download bioinformatic containers from the BioContainers.pro and run them directly using Singularity instructions from the corresponding container’s catalog page.

Brief Singularity guide and examples are available at the Bell Singularity user guide page. Detailed Singularity user guide is available at: sylabs.io/guides/3.8/user-guide

In addition, a subset of pre-downloaded biocontainers wrapped into convenient software modules are provided. These modules wrap underlying complexity and provide the same commands that are expected from non-containerized versions of each application.

On Bell, type the command below to see the lists of biocontainers we deployed.

module load biocontainers
module avail

------------ BioContainers collection modules -------------
      bamtools/2.5.1 
      beast2/2.6.3
      bedtools/2.30.0 
      blast/2.11.0
      bowtie2/2.4.2
      bwa/0.7.17 
      cufflinks/2.2.1
      deeptools/3.5.1
      fastqc/0.11.9
      faststructure/1.0
      htseq/0.13.5
[....]

Link to section ' Example ' of 'BioContainers Collection' Example

This example demonstrates how to run BLASTP with the blast module. This blast module is a biocontainer wrapper for NCBI BLAST.

module load biocontainers
module load blast
blastp -query query.fasta -db nr -out output.txt -outfmt 6 -evalue 0.01

To run a job in batch mode, first prepare a job script that specifies the BioContainer modules you want to launch and the resources required to run it. Then, use the sbatch command to submit your job script to Slurm. The following example shows the job script to use Bowtie2 in bioinformatic analysis.

#!/bin/bash

#SBATCH -A myqueuename
#SBATCH -o bowtie2_%j.txt
#SBATCH -e bowtie2_%j.err
#SBATCH --nodes=1 
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --time=1:30:00
#SBATCH --job-name bowtie2

# Load the Bowtie module
module load biocontainers
module load bowtie2

# Indexing a reference genome
bowtie2-build  ref.fasta ref

# Aligning paired-end reads
bowtie2 -p 8 -x ref -1  reads_1.fq -2 reads_2.fq -S align.sam

To help users get started, we provided detailed user guides for each containerized bioinformatics module on the ReadTheDocs platform

RCAC Biocontainers one ReadTheDocs