Msconvert Wine

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WARNING: This page has not been updated in a long time and is probably obsolete. As of 2019-01, the ProteoWizard developers report that the best way to run the latest msconvert with vendor format conversion on Linux is to use the official Docker image at:

https://hub.docker.com/r/chambm/pwiz-skyline-i-agree-to-the-vendor-licenses

The instructions below are kept for historical purposes, but if you want to install Wine that works with ProteoWizard yourself, it is suggested that you first refer to the official container's Dockerfile:

https://github.com/ProteoWizard/container/blob/master/Dockerfile

WARNING 2: This is a well-documented page on something that did work once at a point in time, but ProteoWizard and its dependencies, the vendor libraries, Wine, and the underlying operating systems are all moving targets. Therefore, the success story related below will likely not work on more recent platforms without additional tricks, or may not work at all. This page should be viewed as a story about something that did work once, and could work again, but may be difficult to get working on your particular platform. Contributions regarding more recent experiences are most welcome.

Proteowizard's msconvert utility is a must have tool for converting mass spectrometry data from almost any proprietary data format into open standards formats (primary mzML and mzXML). While this tool runs on both Windows and Linux, the ability to convert many common instrument formats under Linux is limited due to the need to have vendor specific libraries (dlls) installed. Fortunately it is possible to run the Windows version of msconvert under Linux using Wine, a open source compatibility layer for Windows -- though your mileage may vary.

The following are instructions on how to install and setup Wine under a variety of Linux platforms. These instructions where largely derived from several spctools-discuss emails and a large thanks goes out to the users who posted them (see references below).

1 Requirements
2 Instructions for Ubuntu (Updated 1/9/2013)
- 2.1 Issues/Problems
3 Instructions for CentOS
4 What Works?
5 How can I install windows applications to be shared by multiple users under wine?
6 References

Requirements

You will need to use wine in 32bit emulation mode (basically a 32bit wine even if you are on a 64bit architecture). This is because the .Net and Visual Studio libraries are required and these libraries are installed using a 32 bit installer, even for the 64 bit versions of these libraries. Please also be aware that not all proprietary vendor libraries that are distributed with ProtoWizard are 64 bit hence the 64 bit version of msconvert cannot be used to convert most proprietary files.

Instructions for Ubuntu (Updated 1/9/2013)

The following instructions where developed on a Amazon EC2 instance using Wine 1.5.21 and ProteoWizard 2.1.4131 on the official Ubuntu 12.04 'precise' Amazon Machine Image (AMI).

Please read the notes regarding potential issues following these instructions before executing.

Connect to the system you want to install on. If using ssh use the -X option to ensure display forwarding is set since parts of the setup will prompt you with GUI dialogs asking you to accept licenses.
ssh -X ubuntu@<hostname>
Install the latest 32-bit version of wine
sudo add-apt-repository ppa:ubuntu-wine/ppa
sudo apt-get -y update
sudo apt-get -y install wine1.5-i386
sudo apt-get -y install winetricks
Ensure wine has the correct architecture and set the location of the Windows emulation
export WINEARCH=win32
export WINEPREFIX=~/.wine Default. Choose your location
Use winetricks to configure the Windows emulation
winetricks -q winxp vcrun2005 win7 vcrun2008 vcrun2010
Progressively install the .Net frameworks. While winetricks is suppose to install any older frameworks I found it works better if I did it manually starting from the oldest. Also see note below about sites blocking downloads.
winetricks -q dotnet20 dotnet20sp1 dotnet20sp2
winetricks -q dotnet30
Continue installing the rest of the .Net frameworks
winetricks dotnet30sp1
winetricks dotnet35May fail. Rerunning it a 2nd time worked.
winetricks dotnet35sp1
winetricks dotnet40
Download and install Proteowizard.
Go to http://proteowizard.sourceforge.net/ using a web browser. Click on the downloads link and select the Windows with vendor support option with the tar.bz2 extension. Extract the package and move it to wherever you want to install it.
mkdir pwiz; tar xvf pwiz*.tar.bz2 -C pwiz
Register dll (shouldn't be needed but...)
wine regsvr32 pwiz/MSFileReader.XRawfile2.dll
wine regsvr32 pwiz/CompassXtractMS.dll
Run msconvert
wine pwiz/msconvert.exe

Issues/Problems

Winetricks fails to download a .Net installer

For certain .Net installers winetricks may fail when trying to download the packages. From what I can tell some download sites may be blocking access. Just follow the instructions provided by winetricks. If you happen to be installing on a Amazon EC2 instance you may need to download the files from a system outside the cloud and copy the files to the instance.

dotnet20sp1 install completed but reported missing file

You may observe the following message while installing .Net 20 SP1:

dotnet20sp1 install completed, but installed file ... /c:/windows/assembly/NativeImages_v2.0.50727_32/indexb.dat not found

This appears to be a known issue that can occur with dotnet20sp1 (see [1]). According to the report its harmless and can be fixed by creating creating an empty file as so:

mkdir -p $WINEPREFIX/dosdevices/c:/windows/assembly/NativeImages_v2.0.50727_32
touch $WINEPREFIX/dosdevices/c:/windows/assembly/NativeImages_v2.0.50727_32/indexb.dat

.Net 3.0 installation window "disappears"

If during the installation of .Net 3.0 the installation dialog disappears or appears to hang, look in your "system tray" for the installer icon. This will be the final finish dialog that will need to be clicked through to end the installation.

AB Sciex wiff files throw an exception

When trying to convert AB Sciex wiff files the following error is outputted by msconvert/wine:

[WiffFileImpl::getSampleNames] The type initializer for 'Clearcore2.Data.WiffReader.WiffSampleRun' threw an exception.

At this time msconvert under the wine emulator can't be used to convert AB Sciex wiff files.

Instructions for CentOS

The following instructions where tested using ProteoWizard on a CentOS 6.3 Amazon Machine Image (ami-f0ab24c0). CentOS presents a bigger challenge as you'll need the latest version of Wine and at the time these instructions where written none of the CentOS repositories contained pre-built rpms for it.

Log into the system
Upgrade your system if it hasn't already been
sudo yum -y upgrade
Install necessary packages for building and running wine
yum -y installgroup "Development Tools"
yum -y installgroup "X Window System"
yum -y install libgcc.i686 glibc.i686 glibc-devel.i686 zlib-devel.i686 libX11.i686 libX11-devel.i686 freetype.i686 freetype-devel.i686 freetype-demos.x86_64 freetype-devel.x86_64 libxml2.i686 libxml2-devel.i686 libxslt.i686 libxslt-devel.i686 libXcursor.i686 libXcursor-devel.i686 libpng.i686 libpng-devel.i686 libjpeg.i686 libjpeg-devel.i686 libtiff.i686 libtiff-devel.i686 openssl.i686 openssl-devel.i686 libXrender.i686 libXrender-devel.i686 cabextract
Download the latest development version of wine and install
Get winetricks
wget http://winetricks.org/winetricks
chmod +x winetricks
Install prerequisites
./winetricks winxp vcrun2005 vcrun2008 vcrun2010 dotnet40
Complete steps 8 thru end above

What Works?

The following table shows the results of testing Wine/msconvert with the various different instrument formats available to us. For each format the instrument output was converted using the same version of msconvert installed on Windows 7 and Wine. The program readmzXML was then used to dump a summary of the resulting mzML file and the values compared between systems.

If you have any questions about the testing or have additional results to add please forward them to the spc-tools discussion mailing list.

Wine/msconvert Instrument Formats Tested
Vendor	Model	Acquisition Software	File Type	Result	Notes
ABSciex (Applied Biosystems)	QQQ	Analyst	.wiff file	Fails	Throws exception "The type initializer for 'Clearcore2.Data.WiffReader.WiffSampleRun'"
Agilent	QQQ	MassHunter 2.1	.d directory	Success
Agilent	QTOF	MassHunter 2.1	.d directory	Success
Bruker	Apex, MicrOTOF	unknown	.baf file	Success
Thermo	LTQ Orbitrap XL	Xcalibur 2.4 SP1	.raw directory	Success
Waters	unknown	MassLynx 4.1	.raw directory	Success

How can I install windows applications to be shared by multiple users under wine?

Wine does not currently allow sharing its Windows root (or "prefix") between users, due to the risk of registry corruption from running multiple wineservers simultaneously ([bug #11112]). This means you typically would need to go through and install each set of Windows applications for each user. If you have a lot of users this could become burdensome, however you can create a single prefix and then copy it for each user. (The default wine prefix is ~/.wine). This saves having to run the same installation instructions for each user.

Another option is to write a wrapper script around the whole process. This wrapper script could copy a standardized wine prefix with all of the applications installed into a new temporary prefix owned by the user, set the environment variable WINEPREFIX to point to the temp prefix, run the wine command(s), stop the user's wine server, and then remove the temporary prefix.

One last item, be careful about using NFS with wine. If your home directory is mounted using NFS and shared across systems you could experience some problems running wine on multiple systems in parallel. More information about wine's "windows" partition and NFS:

http://www.winehq.org/pipermail/wine-users/2010-July/076137.html