How to implement a 'commerical' mass spectrometry data processing software on to a Galaxy running on a HPC server/ cluster (to faciliate batch processing)?

Question

[bbmisraccb]

Hello,

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

[GenoMax]

Consider posting this on Galaxy Biostars: https://biostar.usegalaxy.org/

[ablanchetcohen]

I don't understand the question. I have Prohits, an open source mass spectrometry software, and Galaxy running on the same server, but I see no point in linking them. Quite the oppposite. I would much rather have the two programs running on different servers, to eliminate any possibility of one interfering with the other, Although the programs are independent, it's still possible for one to interfere with the other through server overload or human error during configuration changes and updates.

[GenoMax]

I think @bbmisraccb wants to abstract the complexity (perhaps the MS program is command line only) and make it more user friendly (put a GUI in front). There may be a plan to use galaxy as a front end (processing/parsing data from a core) and presenting the results to end-users via galaxy interface.

[GenoMax]

@biswa: Since personal email addresses are not displayed on Biostars I removed your email address that was posted in the text.