IGV-Web#

IGV-Web is the web version of the Integrative Genomics viewer (IGV), which is a visualization tool for genomical data.

VSC clusters that support this app are:

KU Leuven

Accessing data on HPC storage#

Compared to the web application that is available at igv.org/app, the IGV-Web OnDemand app has been customized to facilitate access to data on (VSC) HPC storage.

If you for example have an (indexed) FASTA file on your VSC_SCRATCH, you can select it as a reference genome through Genome > URL ... by entering the absolute file paths in the Genome URL and Index URL fields.

The same approach also applies to the other file types in IGV-Web, such as track files, sample info files and session files. Note that

  • environment variables are not expanded and so for example ${VSC_SCRATCH} cannot be used as part of those URL inputs,

  • exported session URLs and JSON sesion files contain the paths to your selected genome and track files,

  • in this app you can only read from HPC storage, not write to it (session files therefore can only be stored on your local device),

  • the app does not provide access to VSC_HOME.

Saving sessions#

Similar to the instance hosted by the IGV team (igv.org/app), the IGV-Web app will not save your current progress automatically, which means that reloading the tab or closing your browser will clear your session. You can save your current session in different ways:

  • Through the Session > Save menu, to store it as a JSON file on your local device. You can then reopen it later via Session > Local File ... (or via Session > URL ... in case you transferred the file to an HPC storage location).

  • Through the Share menu: copy the generated session URL and save it somewhere. Paste the URL in Session > URL ... to reopen it (pasting the URL in a new browser tab will not work).

  • Through the Bookmark menu, which allows you to create a bookmark for the generated session URL. Also in this case directly opening the URL will not work and you will need to use the Session > URL ... menu instead.

Sharing sessions#

If needed, you may even share such session URLs and session JSON files with co-workers who also use the present IGV-Web OnDemand app. This will, of course, only work if they can also access the associated datasets. On the Tier-2 clusters at KU Leuven, this typically means that the data needs to be stored in a shared staging folder.

Good to know#

  • As the analysis and rendering work happens in your browser, the Slurm job for the app only needs very few resources. These jobs are therefore restricted to run on a single core and with only limited memory and we recommend that you select a suitable partition such as the interactive partition on wICE.

  • You only need a single IGV-Web session in OnDemand even if you want to work with IGV-Web in multiple tabs. Every time you hit ‘Connect’, a new independent tab will open.