README

This project is used to package up an existing WINE environment
configured with proteomics libraries and tools into a single script
that can be copied to new instances.

You are responsible for setting up such an environment intially, but
afterward you should be able to use the resulting script to install on
additional machines or in a way that allows multiple users to use the
environment on the same machine.

The particular use case this was created for was building Ubuntu cloud
images for proteomics using CloudBioLinux (for both desktop and server
applications), but nothing about these scripts is particular to
Ubuntu or really proteomics applications.

Usage:

Once you have configured your local wine instance (in $HOME/.wine),
you simply need to run the bundle_current_env.sh script and that will
create the file setup_proteomics_wine_env.sh, which you can place in
/usr/bin/ (or wherever is convenient) on another Linux instance to
allow others to utilize this environmet.

I have been able to get ProteoWizard with vendor libraries, IDPicker
(http://fenchurch.mc.vanderbilt.edu/software.php), COMPASS
(https://www.chem.wisc.edu/~coon/software.php), multiplierz
(http://blais.dfci.harvard.edu/index.php?id=63), and mzServer
(http://blaispathways.dfci.harvard.edu/mzServer) running under Linux
using this method.

Setting Up Wine for Proteomics Applications:

Proteowizard is probably something you are going to want to setup in
your wine environment. If for no other reason than it in turn sets up
various vendor libraries.

In order to install Proteowizard 2.0.XXXX, one needs to first setup
Microsoft .NET 3.5 and the Visual C 2008 runtime. I believe this can
be done with older versions of Wine (say 1.3 series). The newest
versions of Proteowizard (version 3.XXX.XXX) additionally require
Microsoft .NET 4.0. This use to be problematic, but with the newest
versions for winetricks and wine 1.4 under Ubuntu 12.04 I have been
able to get this to work. Microsoft .NET 4.0 is required for other
tools such as IDPicker also.

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

-----

Download dotnetfx.exe from http://download.cnet.com/Microsoft-NET-Framework-Redistributable-Package-x86/3000-10250_4-10726028.html to $HOME/Downloads.

Download netframework3.exe from http://www.oldversion.com/download-.Net-Framework-3.0.html to $HOME/Downloads.

Download gacutil-net40.tar.bz2 from http://www.mediafire.com/?v8rw5h1ra7maod4 to $HOME/Downloads.

Download the latest 3.X proteowizard to $HOME/Downloads (make sure to download the Windows installer with vendor reader support).

#!/bin/bash

mkdir -p $HOME/.cache/winetricks/dotnet20
mkdir -p $HOME/.cache/winetricks/dotnet30
mkdir -p $HOME/.cache/winetricks/dotnet40
export DOWNLOADS=${DOWNLOADS:-$HOME/Downloads}
export WINEPREFIX=${WINEPREFIX:-$HOME/.wine}
cp $DOWNLOADS/dotnetfx.exe $HOME/.cache/winetricks/dotnet20
cp $DOWNLOADS/netframework3.exe $HOME/.cache/winetricks/dotnet30
cp $DOWNLOADS/gacutil-net40.tar.bz2 $HOME/.cache/winetricks/dotnet40
sudo apt-get install wine
wget http://www.kegel.com/wine/winetricks
chmod +x winetricks  
export WINEARCH=win32; ./winetricks -q winxp dotnet35sp1 dotnet40 vcrun2008
find $DOWNLOADS -name "pwiz-setup-3.*-x86.msi" -print | head -n 1 | xargs wine msiexec /i
wine regsvr32 $WINEPREFIX/drive_c/Program\ Files/ProteoWizard/ProteoWizard*/MSFileReader.XRawfile2.dll


Cleaning Up

You may wish to cleanup your wine environment before creating the
setup script, these are files to consider removing:

rm -rf $WINEPREFIX/drive_c/windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/
rm -rf $WINEPREFIX/drive_c/users/$user/Temp/*