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 [http://www.winehq.org Wine], a open source compatibility layer for Windows -- ''though your mileage may vary''. | + | 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 [http://www.winehq.org 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). | 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). | ||
| Line 26: | Line 26: | ||
| #:./winetricks winxp | #:./winetricks winxp | ||
| #:./winetricks vcrun2008 | #:./winetricks vcrun2008 | ||
| - | #:./winetricks dotnet35 {{pad|3em}}''Will install .Net 2.0 followed by 3.0 then 3.5'' | + | #:./winetricks dotnet35 {{pad|3em}}''Will install .Net 2.0 followed by 3.0 then 3.5, and the 3.5'' |
| # Download and install Proteowizard | # 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: | #: 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: | ||
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| ==== Issues/Problems ==== | ==== Issues/Problems ==== | ||
| - | * If you are trying to install on an Amazon EC2 instance winetricks may fail when trying to download and install vcrun2008 from Microsoft. From what I can tell Microsoft is blocking access from the Amazon Cloud. Just manually download the file from a different system (look for the wget command) and copy it to the EC2 instance. | + | * If you are trying to install on an Amazon EC2 instance winetricks may fail when trying to download and install vcrun2008 from Microsoft. From what I can tell Microsoft is blocking access from the Amazon Cloud. Just manually download the file from a different system (tip, use the wget command suggested by winetricks) and copy it to the EC2 instance. |
| * If during the installation of .Net 3.0 it seems 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. | * If during the installation of .Net 3.0 it seems 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. | ||
| - | * Not working for wiff files as there is a problem with AB Sciex libraries, wine, and possibly .Net 3.5. Trying to determine the exact nature of the problem but it doesn't look promising at the moment. | + | * Currently doesn't work for AB Sciex wiff files as there is a problem with the vendor libraries, wine, and possibly .Net 3.5. Trying to determine the exact nature of the problem but it doesn't look promising at the moment. |
| - | * Lastly should be aware that using .Net 3.5 under wine is still experimental at this time and ProteoWizard elements that make use of this may not work correctly. | + | * Lastly should be aware that using .Net 3.5 under wine is still experimental at this time and the installer may report that it failed. ProteoWizard elements that make use of this may not work correctly. |
| == Instructions for CentOS == | == Instructions for CentOS == | ||
| Line 58: | Line 58: | ||
| #: ''...And wait for a really really long time...'' | #: ''...And wait for a really really long time...'' | ||
| # Run Steps 3 on from the ubtuntu section | # Run Steps 3 on from the ubtuntu section | ||
| + | # Register the dll's | ||
| + | #: cd pwiz {{pad|3em}}''Or whichever directory you installed Proteowizard in'' | ||
| + | #: wine regsvr32 MSFileReader.XRawfile2.dll | ||
| + | #: wine regsvr32 CompassXtractMS.dll | ||
| == What Works? == | == What Works? == | ||
Revision as of 17:29, 30 June 2011
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).
Contents |
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 .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. 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
The following instructions where tested using ProteoWizard 2.1.2785 on a Ubuntu 11.10 'natty' Amazon Machine Image running Wine 1.2.2 (See http://cloud.ubuntu.com/ami/ for more AMI options).
 | 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 root@system
- Update/install rpms
- sudo apt-get update
- sudo apt-get -y install wine cabextract
- Use winetricks to install required Windows resources
- wget http://www.kegel.com/wine/winetricks
- chmod 755 winetricks
- ./winetricks winxp
- ./winetricks vcrun2008
- ./winetricks dotnet35 Will install .Net 2.0 followed by 3.0 then 3.5, and the 3.5
- 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
Issues/Problems
- If you are trying to install on an Amazon EC2 instance winetricks may fail when trying to download and install vcrun2008 from Microsoft. From what I can tell Microsoft is blocking access from the Amazon Cloud. Just manually download the file from a different system (tip, use the wget command suggested by winetricks) and copy it to the EC2 instance.
- If during the installation of .Net 3.0 it seems 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.
- Currently doesn't work for AB Sciex wiff files as there is a problem with the vendor libraries, wine, and possibly .Net 3.5. Trying to determine the exact nature of the problem but it doesn't look promising at the moment.
- Lastly should be aware that using .Net 3.5 under wine is still experimental at this time and the installer may report that it failed. ProteoWizard elements that make use of this may not work correctly.
Instructions for CentOS
The following instructions where tested using ProteoWizard 2.1.2785 on a CentOS 5.5 Amazon Machine Image (ami-68f80f01). 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.
- Upgrade your system if it hasn't already been
- Install necessary packages for building and running wine
- 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 and build wine (using -X)
- CC=/usr/bin/gcc44
- wget http://download.hostedgameservers.com/install-wine1.2.2.sh
- chmod 777 install-wine1.2.2.sh
- ./install-wine1.2.2.sh
- ...And wait for a really really long time...
- Run Steps 3 on from the ubtuntu section
- Register the dll's
- cd pwiz Or whichever directory you installed Proteowizard in
- wine regsvr32 MSFileReader.XRawfile2.dll
- wine regsvr32 CompassXtractMS.dll
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.
| Vendor | Model | Acquisition Software | Output Type | Result | Notes |
|---|---|---|---|---|---|
| Applied Biosystems (ABSciex) | QQQ | Analyst | .wiff file | Fails | Requires .Net 3.5 which doesn't function under wine. |
| Agilent | QQQ | MassHunter 2.1 | .d directory | Success | |
| Agilent | QTOF | MassHunter 2.1 | .d directory | Success | |
| Waters | ? | MassLynx 4.1 | .raw directory | Success |
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 having to run the same installation instructions for each user.
More information about wine's "windows" partition and NFS:
References
- 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
