UCSC Genome Browser and IGV access for data on O2

Owned by Andy Bergman
Last updated: Jan 25, 2024
2 min read

Research Computing provides a website for users of the O2 cluster to present their data via HTTP for use with external genome browsers such the UCSC Genome Browser.

IGV Users please read:

You can run IGV on O2 itself to analyze data from any location on O2, without needing any additional group access. To do this, just login via the O2 Portal which is designed to easily run GUI applications.

User Access

(this is only needed if you do require presenting O2 data to applications outside of O2)

To access this tool, the user must have an O2 cluster account and be a member of the group: genomebrowser-uploads

  • You can apply for an O2 account via our online request form (HMS ID login is required to use the form).

  • To add your O2 account to group genomebrowser-uploads, please send us a support request: rchelp@hms.harvard.edu

How to use the website

Once you have an O2 account with access, you can make your data presentable with the following steps:

  1. Create your personal data directory under: /n/groups/genomebrowser-uploads/data/

    1. For example (e.g. for user abc123): /n/groups/genomebrowser-uploads/data/abc123

  2. Copy your data files under the personal directory:

    1. For example: /n/groups/genomebrowser-uploads/data/abc123/mydata.bam

    2. Make sure your data files are set as world-readable (typically the default), so the web server can access them.

  3. View your data via this public URL: http://genomebrowser-uploads.hms.harvard.edu/data/[USER_DIRECTORY]/[USER_DATA]

    1. In this example, the URL would be: http://genomebrowser-uploads.hms.harvard.edu/data/abc123/mydata.bam

  4. Please remove your data files once analysis has been completed!

Misc

  • There is no file expiration policy at this time under the data directory, so we ask all users to please remove their data once analysis has been completed!

  • A maximum storage quota (for all user data combined) is maintained on the data directory, currently set at 15 TiB.

Digital Accessibility