Genomics Virtual Lab
In addition to our role in hosting and managing the national Galaxy Australia service, RCC is an active contributor to the development of the Genomics Virtual Laboratory (GVL), which is software for a virtual server.
Users who want to host and manage their own instance of Galaxy (or any of the other analysis systems listed below) can easily do this by launching their own GVL server instance within the Nectar cloud or other OpenStack and EC2 compatible clouds.
Each GVL instance provides a standard suite of genomics analysis tools pre-installed:
- Galaxy: Galaxy is an open source, Web-based platform for data-intensive biomedical research supporting reference data sets, thousands of tools, workflow development and management.
- Command line access: Each GVL instance runs on Linux. Many Galaxy-installed bioinformatics tools are also accessible from command line.
- VNC Desktop: A browser-based remote desktop for Linux.
- RStudio: Programming and analysis environment for the R language. GVL instances come with many R packages from the Bioconductor Project pre-installed.
- JupyterHub: Jupyter is an interactive programming and analysis environment for Python and other languages, capable of producing interactive analysis documents.
- Pathway Tools: Pathway Tools is a comprehensive symbolic systems biology software system that is associated with the BioCyc database collection.
- GVL Dashboard: The homepage of a GVL instance. It shows the status of each service and gives a link to each running service, together with login details for that service.
- Cloudman: Cloudman enables administrative control over the GVL virtual machine. It also allows the admin to add worker nodes to their instance to build a virtual cluster-in-the-cloud.
Additionally, a number of optional add-ons can also easily be installed on a GVL server:
- LOVD: Leiden Open Variant Database.
- CPipe: CPipe is a variant detection pipeline designed to process high-throughput sequencing data.
- SMRTPortal: PacBio’s open source software suite for single molecule, real-time sequencing.
- Pancancer BWA-Mem: The SeqWare workflow for the TCGA/ICGC PanCancer project that aligns whole genome sequences with BWA-Mem.
- IRIDA: Public Health Agency of Canada’s IRIDA server system.
- Web Apollo: Genome annotation editor.
Note that you do need to manage your own instance yourself (i.e. undertake all the systems administration tasks etc.).
If you want to launch your own GVL, follow the instructions here.
Email help@genome.edu.au to arrange a discussion about how you could use a self-managed GVL in your research.