Biorunner: a collection of bioinformatics tools

Introduction

Biorunner is a way to quickly install a controlled set of tools widely used in Life Sciences and Bioinformatics. For researchers, installing all tools manually can be challanging; with this collection, you have one chorerent set of all tools, with known versions, in a single image file.

Although developed for use on high-performance compute clusters in supercomputing centres, you can install the tools on a local workstation or even on your own computer, to have exactly the same environment locally as on the supercomputing centre.

Biorunner uses Singularity [1] for packaging all applications in a single image, and also needs it where running the applications. Installing Biorunner involves putting the image your PATH environment, adding a wrapper script that runs commands inside a Singularity container, and symbolic links for all commands availble in the Biorunner image, pointing to the wrapper script.

Installing a pre-built image

Rebuilding an image

For building your own image, you need, on the system where you are building the image:

• singularity; version 3 or later
• root access
• at least 5 Gigabytes of free disk space
• a good network connection

Now, become root; as root

1. first, set the environment variable SINGULARITY_TMPDIR to a path where you have at least 5 GB of free disk space.

   If you do not set this variable, singularity will use ''/var/tmp''.

   To set it to, for example, a directory called "/scratch", do """ export SINGULARITY_TMPDIR=/scratch """

2. Do """ singularity build biorunner-2019b.sif biorunner.def """

That is it! This may take a while, but after the build, you have a container image file "biorunner-2019b.sif". See INSTALLATION for further installation instructions.

Applications offered through Biorunner

Thefollowing applications are exposed through Biorunner:

From Ubuntu

• bowtie2
• samtools
• ncbi-blast2
• minimap
• miniasm
• fastqc
• poretools
• clustal Omega
• clustal x
• SPAdes

Through custom builds

• Deepbinner
• Nanopolish
• trimAl
• Filtlong
• Racon
• minimap2
• Pilon
• Unicycler
• Mauve
• PhyML, SMS-PhyML
• Centrifuge
• Hmmer
• Prokka (v1.14.6)
• nanopack

Software version list

|-----------------------------|--------------|

Package	Version
SMS-PhyML	1.8.4
Prokka	1.14.6