Purdue University

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.

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

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

$ module purge
$ module load modtree/cpu
$ module load biocontainers 
$ module avail 

Once module loaded biocontainers, you can run your code as with normal non-containerized applications. This section illustrates how to use SLURM to submit a job with a biocontainers program.

#!/bin/bash
# FILENAME:  myjobsubmissionfile

#SBATCH -A myallocation       # allocation name
#SBATCH --nodes=1             # Total # of nodes 
#SBATCH --ntasks-per-node=1   # Number of MPI ranks per node 
#SBATCH --time=1:30:00        # Total run time limit (hh:mm:ss)
#SBATCH -J myjobname          # Job name
#SBATCH -o myjob.o%j          # Name of stdout output file
#SBATCH -e myjob.e%j          # Name of stderr error file
#SBATCH -p wholenode          # Queue (partition) name
#SBATCH --mail-user=useremailaddress
#SBATCH --mail-type=all       # Send email to above address at begin and end of job 

# Manage processing environment, load compilers, container, and applications.
module purge
module load modtree/cpu
module load biocontainers
module load applicationname
module list

# Launch code
./myexecutablefiles