Question: How to implement a 'commerical' mass spectrometry data processing software on to a Galaxy running on a HPC cluster/ server (to faciliate batch processing)?
gravatar for Biswapriya
14 months ago by
United States
Biswapriya120 wrote:


I want to run a commercial mass-spectrometry software (from GC-MS, LC-MS instrument vendors) on a cluster and also integrate into our existing Galaxy server! Computational load wise the server is huge and have sufficient capabilities. We have personnel who can do it but need to suggest them/ provide instructions.

Questions are:

  1. How to get the commercial tool(s) integrated into Galaxy workflow?
  2. What do we need from the commercial software provider?
  3. How to automate or semi-automate the entire process, like file upload, batch processing, obtaining results so that the outputs are human readable (say a .csv outputs etc.)!
  4. What expertise/ softtools does one need to have access to be able to furnish this work?

Looking forward to your advice.

Thanks, Biswa

ADD COMMENTlink modified 14 months ago by Andrew Patterson180 • written 14 months ago by Biswapriya120
gravatar for Andrew Patterson
14 months ago by
Penn State University
Andrew Patterson180 wrote:

hi Biswa

I will pass this information on to Dr. Anton Nekrutenko here at Penn State. He has been interested in setting up more metabolomic workflows in Galaxy. You might also check which has a lot of dedicated Galaxy discussions.


ADD COMMENTlink written 14 months ago by Andrew Patterson180
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