Msconvert Wine

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http://www.winehq.org/pipermail/wine-users/2010-July/076137.html http://www.winehq.org/pipermail/wine-users/2010-July/076137.html
 +
 +3.3. 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.
== Instructions for CentOS 5.5 == == Instructions for CentOS 5.5 ==

Revision as of 19:49, 8 February 2011

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.

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 this:

http://groups.google.com/group/spctools-discuss/browse_thread/thread/604745729ac0e541
http://groups.google.com/group/spctools-discuss/browse_thread/thread/bb2a608ad31f77dd/868fab027488bd09?hl=en&lnk=gst&q=wine#868fab027488bd09
http://groups.google.com/group/spctools-discuss/browse_thread/thread/2d98145b42479cb0/f8d80a25d1f8583c?hl=en&lnk=gst&q=wine#f8d80a25d1f8583c

Contents

Gotchas

You will need to use wine in 32bit emulation mode. 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 64 bit

The following instructions where tested on a Ubuntu Amazon Machine Image. See http://uec-images.ubuntu.com/releases/10.10/release/ for the image id.

  1. 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
  2. Update/install rpms
    sudo apt-get update
    sudo apt-get install wine
    sudo apt-get install cabextract
    wget http://www.kegel.com/wine/winetricks
    chmod 755 winetricks
    ./winetricks winxp
    ./winetricks vcrun2008
    ./winetricks dotnet20
  3. Download and install Proteowizard
    Go to http://proteowizard.sourceforge.net/download.html using a web browser. Click on the artifacts link for the Windows x86 (or x86_64) build. When the TeamCity login page is displayed log in as guest using the link provided. 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

Note: you will get a click through license in a GUI dialog the first time you try to process any Agilent data

More of interest. Setting up wine's "windows" partition and NFS:

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

3.3. 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.

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

References

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine"
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