Msconvert Wine

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Proteowizard's msconvert utility is a must have tool for converting MS/MS data from almost any proprietary MS/MS 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 formats under Linux is unavailable 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 Gotchas
2 Instructions for Ubuntu
3 Instructions for CentOS 5.5
4 References

Gotchas

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 .Net and Visual Studio libraries are required and these libraries are installed using a 32bit installer, even for the 64 bit versions of these libraries.

Instructions for Ubuntu

The following instructions where tested on a Ubuntu 11.10 'natty' Amazon Machine Image running Wine 1.2.2 (See http://cloud.ubuntu.com/ami/ for more AMI options).

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 root@system
Update/install rpms
sudo apt-get update
sudo apt-get -y install wine cabextract
wget http://www.kegel.com/wine/winetricks
chmod 755 winetricks
./winetricks winxp
./winetricks vcrun2008
./winetricks dotnet35
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 (not the 64 bit version as the required vendor libraries aren't 64 bit). Download the file 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
How can I install applications to be shared by multiple users?

Wine does not currently allow sharing its configuration ("prefixes") between users, due to the risk of #:registry corruption from running multiple wineservers simultaneously (bug #11112). At present, applications #:must be installed separately for each user.

However, you can copy Wine prefixes; you can install everything to one prefix, then make a copy of it in each #:user's home directory. This saves running installers repeatedly.

More information about wine's "windows" partition and NFS:

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

Instructions for CentOS 5.5

CentOS presents a bigger challenge, as you'll need the latest version of Wine and at the time these instructions where written there aren't pre-built rpms for it.

AMI: ami-01996f68

rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm

rpm -Uvh http://apt.sw.be/redhat/el5/en/x86_64/rpmforge/RPMS/rpmforge-release-0.5.2-2.el5.rf.x86_64.rpm

yum -y update

yum -y install xauth cabextract fontconfig gcc44 rpm-build

wget ftp://ftp.pbone.net/mirror/ftp.sourceforge.net/pub/sourceforge/h/project/hp/hphp/CentOS%205%2064bit/RPM/flex-2.5.35-7.x86_64.rpm

rpm -Uvh flex*

Log out, then log back in

CC=/usr/bin/gcc44 rpmbuild --define "_without_gstreamer 0" --nodeps

wget http://download.hostedgameservers.com/install-wine1.2.2.sh chmod 777 install-wine1.2.2.sh vi install-wine1.2.2.sh # remove the download, configure and make commands

rpm --nomd5 -ivh http://apt.sw.be/redhat/el5/en/source/wine-1.3.7-1.rft.src.rpm

ProteinProphet

MassLynx ./winetricks mfc42 wine regsvr32 DACServer.dll