Each GVL instance comes with pre-installed bioinformatics tools and reference data, which can be used through several different interfaces.
The various platforms and analysis environments installed on each GVL instance are described below.
Each of these services is accessible from your instance's GVL Dashboard.
On GVL version 4.0 and later, these components should all already be installed. On earlier versions such as 3.05, Galaxy and CloudMan will already be installed, but you will need to activate some other utilities by following the instructions in v3.05 of the README in our GitHub repository
The GVL Dashboard is the home page of your GVL instance. You can find it by directing your web browser to the IP address or URL or your launched instance.
It shows the status of each service and gives a link to each running service, together with login details for that service.
CloudMan gives you administrative control over your virtual machine. It also allows you to add worker nodes to your instance to build a virtual cluster-in-the-cloud. You can find your instance's CloudMan interface at http://<your_instance_IP>/cloud.
You can find out more about CloudMan here.
Galaxy is a web-based platform for biomedical research. Each launched GVL instance comes with its own Galaxy server, which you can access from the GVL dashboard or at http://<your_instance_IP>/galaxy.
Or, if you are an Australian researcher, you can use one of our Galaxy servers instead. You can find out more about Galaxy at the Galaxy Project site.
Your GVL instance runs on linux, which you have full administrative access to. Many Galaxy-installed bioinformatics tools are also accessible from command line.
For ordinary use, ssh in with ssh researcher@<your_instance_IP> or for administrative purposes, ssh in with ssh ubuntu@<your_instance_IP>.
VNC desktop is a browser-based remote desktop for linux. You can log in using your linux credentials, as user researcher for research purposes, or user ubuntu for administrative purposes.
You can access your VNC interface from the GVL dashboard or at http://<your_instance_IP>/vnc.
RStudio Server gives browser-based access to RStudio, the popular programming and analysis environment for the R programming language. The R-studio interface is accessible from the GVL dashboard or at http://<your_instance_IP>/rstudio.
You can find out more about RStudio here, and the R programming language here.
GVL instances come with many R packages from the Bioconductor Project pre-installed.
Jupyter Hub is an interactive programming and analysis environment for the Python and other programming languages, capable of producing interactive analysis documents.
You can find out more about Jupyter Hub here.
Currently the Python 2.7 and Python 3.5 kernels are installed. It is accessible from the GVL dashboard.
Various add-ons and extra services can also be installed on your GVL server. Each one of these is installed by clicking on a single install button from the GVL dashboard Admin page. Once installed, each service is added to the GVL dashboard for easy accessibility.
Currently the extra services available are:
This package can be used to install the Leiden Open Variant Database (LOVD).
This package can be used to install Cpipe, a variant detection pipeline designed to process high-throughput sequencing data, with the purpose of identifying potentially pathogenic mutations.
This package can be used to install PacBio's open source software suite for single molecule, real-time sequencing. PacBio recommends the use of a 16 core instance with 64GB of RAM (or higher) for this package.
This is the SeqWare workflow for the TCGA/ICGC PanCancer project that aligns whole genome sequences with BWA-Mem. It also reads/writes to GNOS (optionally), the metadata/data repository system used in the project. After installation, the workflow can be executed through the commandline. More information can be found here
This package can be used to install the Public Health Agency of Canada's IRIDA server system. The Integrated Rapid Infectious Disease Analysis (IRIDA) project is a Canadian-led initiative to build an open source, end-to-end platform for infectious disease genomic epidemiology.
This package can be used to install the Apollo Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin. See Apollo - Genome Architect for details