Installation Guide

MzIO contains 7 different projects. 3 of those projects are essential for most practical applications. Those would be MzIO (basic functions), MzIO.Processing (data processing functions) and MzIO.SQL (functions to interact with the SQLite database). The other 4 projects are for 4 different file formats. Currently supported formats are Wiff (wiff), Bruker (baf) , Thermo Fisher (raw) and MzML (xml). The readers for those formats can be installed individually.

Currently, the nuget packages are only available at our github nuget branch. At a later point they will be released at nuget.org. You can either install them from there or build the binaries yourself.

Building the binaries yourself

• Install .Net Core SDK
• Install the dotnet tool fake cli by dotnet tool install fake-cli -g for global installation, or dotnet tool install fake-cli --tool-path yourtoolpath.
• Download the RawFileReader nuget packages for the .net version from Thermo Fisher Scientific and place them in lib/ThermoFisher.
• Open the console and navigate to the root folder of the repository. Then run the command fake build

Important notes:

Wiff-Reader

• You have to run the projects in 32 bit mode for the Wiff-Reader to work properly.
• You need a Clearcore2 license for the Clearcore2 dlls used in this project.
  • A dummy file for the license which can be replaced is already located at ..\src\MzIO.Wiff\License.

Bruker-Reader

• You have to specify the platform on which the project runs, since bruker uses a different dll for 32 bit and 64 bit.
• You need to install Visual C++ Redistributable for Visual Studio 2012 Update 4.

Using the prerelease packages from the nuget branch

If you are using paket, add the following line to your paket.dependencies file:

git https://github.com/CSBiology/MzIO.git nuget Packages: /

you can then access the individual packages:

nuget MzIO

nuget MzIO.Processing

nuget MzIO.Wiff

nuget MzIO.Bruker

nuget MzIO.Thermo

nuget MzIO.MzML

Important notes:

• The important notes for installing the binaries yourself apply to the nuget packages as well.
• For the package MzIO.Thermo you need to do the following steps if you are managing your dependencies with paket:
  • Download the RawFileReader nuget packages for the .net version from Thermo Fisher Scientific and place them in lib/ThermoFisher or another folder of your choice
  • Add
    source lib/ThermoFisher (source may vary based on your chosen location)
    nuget ThermoFisher.CommonCore.BackgroundSubtraction
nuget ThermoFisher.CommonCore.Data
nuget ThermoFisher.CommonCore.MassPrecisionEstimator
nuget ThermoFisher.CommonCore.RawFileReader
    to your paket.dependencies file
  • Run the command paket update, followed by fake build