Msconvert Wine
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| - | Proteowizard's msconvert utility is a must have tool for converting MS/MS data in almost any proprietary MS/MS data run into almost any of the commonly used open formats. While this tool is available 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). Fortunately it *is* possible to run the Windows version of msconvert under Linux using [http://www.winehq.org Wine], a open source compatibility layer. | + | 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. |
| + | 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: | ||
| - | == Instructions for Ubuntu == | + | 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 | ||
| - | http://uec-images.ubuntu.com/releases/10.10/release/ | + | == Gotchas == |
| - | Tested with 64 bit image | + | 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. |
| - | ssh -X | + | |
| + | == 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. | ||
| + | |||
| + | # Use -X to ensure display forwarding is set. Part of the setup will prompt you with GUI dialogs asking you to accept licenses. | ||
| + | ssh -X root@system | ||
| : sudo apt-get update | : sudo apt-get update | ||
| Line 22: | Line 31: | ||
| 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: | 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 # cause pwiz is rude and pollutes | + | |
| - | cd pwiz | + | # cause pwiz is rude and pollutes the current directory |
| - | tar xvf ../pwiz*.tar.bz2 | + | mkdir pwiz; tar xvf pwiz*.tar.bz2 -C pwiz |
| - | Note: may want to process a .d file (at the very least) to click through the license. | + | Note: you will get a click through license in a GUI dialog the first time you try to process any Agilent data |
| + | == 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 | |
| - | http://teamcity.labkey.org:8080/repository/download/bt83/24694:id/pwiz-bin-windows-x86-vc90-release-2_1_2464.tar.bz2 | + | where written there aren't pre-built rpms for it. |
| - | + | ||
| - | == Instructions for CentOS == | + | |
| AMI: ami-01996f68 | AMI: ami-01996f68 | ||
| : rpm -Uvh http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-4.noarch.rpm | : 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 update | ||
| : yum -y install xauth cabextract fontconfig gcc44 rpm-build | : yum -y install xauth cabextract fontconfig gcc44 rpm-build | ||
| - | : rpm -Uvh http://rpm.pbone.net/index.php3/stat/4/idpl/14565045/dir/centos_other/com/flex-2.5.35-7.x86_64.rpm.html | ||
| : 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 | : 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* | : rpm -Uvh flex* | ||
| - | : wget http://downloads.sourceforge.net/project/wine/Source/wine-1.2.1.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fwine%2F&ts=1295048793use_mirror=cdnetworks-us-1 | ||
| - | : rpm -Uvh http://apt.sw.be/redhat/el5/en/x86_64/rpmforge/RPMS/rpmforge-release-0.5.2-2.el5.rf.x86_64.rpm | ||
| - | : ./configure --enable-win64 CC=/usr/bin/gcc44 | ||
| - | log out log back in | ||
| - | DAMMIT Microsoft packages the Visual C++ libraries and .New libraries with a 32bit installer which WILL NOT run under wine64. | + | Log out, then log back in |
| CC=/usr/bin/gcc44 | CC=/usr/bin/gcc44 | ||
| rpmbuild --define "_without_gstreamer 0" --nodeps | rpmbuild --define "_without_gstreamer 0" --nodeps | ||
| - | 32bit on 64.... | ||
| wget http://download.hostedgameservers.com/install-wine1.2.2.sh | 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 | rpm --nomd5 -ivh http://apt.sw.be/redhat/el5/en/source/wine-1.3.7-1.rft.src.rpm | ||
| - | yum install freetype.i386 | ||
| - | configure: OpenCL 32-bit development files not found, OpenCL won't be supported. | ||
| - | |||
| - | configure: libhal/libdbus 32-bit development files not found, no dynamic device | ||
| - | support. | ||
| - | configure: libgnutls 32-bit development files not found, no schannel support. | ||
| - | configure: libv4l 32-bit development files not found. | ||
| - | configure: libgphoto2 32-bit development files not found, digital cameras won't | ||
| - | be supported. | ||
| - | configure: gstreamer-0.10 base plugins 32-bit development files not found, gstre | ||
| - | amer support disabled | ||
| - | configure: libcapi20 32-bit development files not found, ISDN won't be supported | ||
| - | . | ||
| - | configure: libmpg123 32-bit development files not found (or too old), mp3 codec | ||
| - | won't be supported. | ||
| - | configure: libopenal 32-bit development files not found (or too old), OpenAL won | ||
| - | 't be supported. | ||
| - | |||
| - | configure: WARNING: libxml2 32-bit development files not found, XML won't be sup | ||
| - | ported. | ||
| - | |||
| - | configure: WARNING: libxslt 32-bit development files not found, xslt won't be su | ||
| - | pported. | ||
| - | |||
| - | configure: WARNING: GetText 32-bit development files not found. Internationaliza | ||
| - | tion won't be fully supported. | ||
| - | |||
| - | configure: Finished. Do 'make' to compile Wine. | ||
| + | ProteinProphet | ||
| MassLynx | MassLynx | ||
Revision as of 00:10, 27 January 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.
- Use -X to ensure display forwarding is set. Part of the setup will prompt you with GUI dialogs asking you to accept licenses.
ssh -X root@system
- 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
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:
- cause pwiz is rude and pollutes the current directory
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
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
