Dear list,

Our analysis pipeline is normally fed with proprietary raw file types from mass spectrometry instruments. These can currently only be read on windows systems where vendor DLLs are installed.

Since Cloudman/Galaxy does not interface with Windows nodes out of the box, I implemented a conversion tool wrapper that instantiates windows nodes on EC2 and lets them convert the raw files. It currently only does this, but there would of course be room for a number of other tools on the same windows image.

I know there are limitations such as Amazon's 20 node limit and the nodes not being controlled in Cloudman, but I wonder if my implementation would cause any serious problems with running this. Problems like security, etc (after all, the tool wrapper curls the user data to get the AWS access/secret keys. If anyone has comments on it, I'd love to hear them.

Current code for the windows image can be found on:

And the tool that creates the windows node is on:


Scientific programmer
Mass spec analysis support @ BILS
Janne Lehtiö / Lukas Käll labs
SciLifeLab Stockholm

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