Streamline your bioinformatics workflows with BioSAILs!
BioSAILs stands for Bioinformatic Standardized Analysis Information Layers, and it incorporates the following completely decoupled systems,
- Biox – Which is the analysis templating system.
- HPCrunner – The workflow submission system.
- Bioinformatics software management system based on BioConda.
We all know that there is no such thing as a “one size fits all” when it comes to bioinformatics analysis. With BioSAILs, our aim is not to provide a “push-button” type solution, but rather a system that can accommodate the vast complexity of running analysis pipelines/workflows.
BioSAILs has been developed by a small Core Bioinformatics team that is focused on managing and analyzing substantial amounts of high throughput sequencing data. When designing BioSAILs, we needed to take account of the following,
- Design a system that is agnostic as to the OS/Hardware combination it was running on (as long as it’s UNIX based).
- Enable reproducible research.
- Have a simple command line interface.
- Flexible and easy to modify analysis workflows.
- Can submit and track analysis workflows whether it’s on a high performance computing cluster, or a standalone Laptop.
- Agnostic as to where bioinformatics software is installed.
BioSAILs has enabled us to analyze data from Metagenomics (shotgun/amplicon), RNAseq, Genome/Exome resequencing, de novo genome/transcriptome, epigenome (CHiPseq/ATACseq), and we believe it is now at a stage where the wider scientific community would benefit from using it. We hope to have a catalogue of community and in-house developed workflows that can be reused and adapted, without the need to write pipelines from scratch.
On this website, you will find everything that we have put together in order to make it as easy as possible for you to start using BioSAILs. We also have a section dedicated to setting up a bioinformatics infrastructure.
If this is your first visit, we suggest you start with this guide here, which will take you from “No BioSAILs” all the way to reading an interesting paper and translating that into an analysis workflow.
Install BioSAILs Quick Start
Install on Linux
conda install -c bioconda -c conda-forge perl-hpc-runner-command perl-biox-workflow-command
Install on MacOSX
conda install -c bioconda -c conda-forge perl-app-cpanminus
cpanm HPC::Runner::Command BioX::Workflow::Command