How to implement a 'commerical' MS data processing software in Galaxy ?

July 04, 2016, 10:44:12 AM

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:

How to get the commercial tool(s) integrated into Galaxy workflow?
What do we need from the commercial software provider?
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.)!
What expertise/ softtools does one need to have access to be able to furnish this work?

Looking forward to your advice.

Thanks and regards,
Biswa

Re: How to implement a 'commerical' MS data processing software in Galaxy ?

Reply #1 – September 06, 2016, 05:10:33 AM

You need to check if the commercial tools licensing would allow you to do it, even if you plan to run it locally.
You can generate a "tool config file" or "wrapper" and share that if you wish (without the commercial tool).
There are many tutorial and wikis on this and larger community to ask questions. @Ralf Weber know quite a lot more.
Best Wishes,
Reza