Sunday, May 29, 2011

Javascript File Browser for Server-Side Files

Problem - Galaxy

Galaxy is a web-based bioinformatics toolkit that allows users to create customized data analysis pipelines. It is becoming an extremely common tool, especially in the sequencing field. The project has one major flaw: it is difficult to get large data files into the system. Uploading 2G files (generated from sequencing runs) through a browser is not a workable solution.

Solution - iRods

iRods is a virtual file system commonly used to transfer and share files in the scientific community. It abstracts the storage details and provides tools for access control, sharing, metadata tracking, file type conversion, and high performance multi-threaded file transfer.


Myself and co-workers Fred Bevins and Susan Miller were tasked with integrating iRods and Galaxy during the iRods code sprint hosted by iPlant in April. My share of the work was a client-side Javascript file browser. The file browser allows users to browse and select server side files. The version I built talks to the iPlant Foundational API, which exposes iRods directories and files. Other back-ends could easily be added to allow the file browser to talk with a standard file system, or any other file repository. Fred and Susan worked on integrating the file browser into Galaxy, which allows Galaxy users to browse and select files in an iRods repository for use in an analysis. The javascript code is available now, and the Galaxy integration code should be available sometime soon.


  1. Hi Dave,

    Integration of iRODS with Galaxy is very valuable. We have been thinking of a way to do this for some time.

    Is this planned as a project that will live for a while, with support, or is it just a one off to see if it can be done?

    We would be very interested in the working code when it is available.


  2. The BCF team is working on putting together a complete package. I'm not sure what the timeline for it is.

  3. I'll donate $5 for beer to help speed it along. :)