Hi Matt,

It would be possible to add a new module to work with MSGF+ or other search engines, but it would be a lot easier to integrate support into our existing MS2 module directly. There are a number of key classes that are not currently exposed outside of the MS2 module that you'd want to be able to extend and use.

I recently added support for Comet, another MS2 search engine. It's probably the best template for what would be involved in adding another search engine. You can find the code here:

<LABKEY_ROOT>\server\modules\ms2\src\org\labkey\ms2\pipeline\comet

You'd effectively want to clone most of those classes and adapt them to work with MSGF+ instead. I'm not directly familiar with it, so I don't know specifically what would be required, but examples of likely work items include creating the parameters file and/or command-line arguments to run the program, converting file formats for inputs or outputs to match expectations, etc.

Starting points in the documentation include:

Set up a Development Machine: https://www.labkey.org/wiki/home/Documentation/page.view?name=build

Java Modules: https://www.labkey.org/wiki/home/Documentation/page.view?name=buildingModule

LabKey Open Source Project: https://www.labkey.org/wiki/home/Documentation/page.view?name=openSourceProject

I hope this helps with some useful pointers.

Thanks,
Josh