Readw.exe for Linux

[Charles]

Hello,

I've installed and used TPP v4.3.1 on my personal computer running
Win7 for a couple of months now and tested it with a couple of test
sample files and found everything to be running fine. I would now
like to now transfer this pipeline onto a linux server in order to
make the pipeline available to the rest of the lab. I've installed
the same version for linux just fine, but while trying to write a
script to automate a lot of the data conversion/management processes,
I found that that there isn't a "readw" program in "/tpp/bin". I've
searched around online and found an obscure link for the linux version
and found that it's called "t2x", but searing on this forum indicated
that it's a depreciated version and is no longer supported.

I was wondering if there's an official readw for linux boxes somewhere
on the horizon or some work around to run a windows executable in a
linux environment. Right now, I need to transfer RAW files from the
server to my computer, convert them into mzXML, and then transfer the
files back. These are two completely unnecessary transfers, which
take up a lot of time especially since these are rather large files
(profile Orbitrap data), which basically double in size for the mzXML
format.

Thanks,
Charles

[Jimmy Eng]

Christian,

readw is and will always be a windows app because it makes use of
windows DLLs supplied by Thermo to read the raw files. If you really
want to get away from the data transfers (which you can automate ...
search for 'conversion server' on this group to see Greg Taylor's
recipe for installing openssh on a Windows box), you'll have to look
into an application like Wine or the commercial version CrossOver. I
believe the latter is actively being used for running readw on linux
on the Sorcerer box by Sage-N and I haven't heard any reports of
problems. On the other hand, I haven't heard of a successful Wine
implementation yet for what that's worth.

And in case you're not already using compression, add the '--compress'
command line option to compress the peak lists.

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[Angel]

Y, I have wine working with msconvert from proteowizard.

# NOT COVERED: You need to install wine as per you linux distro
# Then use winetricks to get some deps
curl -O http://www.kegel.com/wine/winetricks
chmod 755 winetricks
./winetricks winxp
./winetricks vcrun2008
./winetricks dotnet20

# then get msfilereader from thermo
curl -O http://sjsupport.thermofinnigan.com/software/msfilereader_ver-13_04-14-2009_Setup.zip
unzip msfilereader_ver-13_04-14-2009_Setup.zip
wine msiexec /q /i /msfilereader_ver-13_04-14-2009_Setup/setup_msi/
thermo\ install.msi

# then get the latest windows version of pwiz
curl -L -o pwiz.zip
http://sourceforge.net/projects/proteowizard/files/proteowizard/1.6.0/pwiz-1.6.0-tools-windows-i386.zip/download
unzip -d pwiz pwiz.zip

You then run msconvert.exe like so

wine pwiz/msconvert.exe MyRawFile.RAW

Here is an example outputting 32 bit intensity compressing all binary
data arrays

wine pwiz/msconvert.exe --int32 -z MyRawFile.RAW

-angel

[Angel]

Hi all,

Pat of Sage-N contacted me about wine + pwiz. He could not get it to
work, so I did a bit more digging.

For winetricks to install dotnet20 and vcrun2008, you must first
install X11 libraries and connect to the linux server forwarding X11

ssh -X m...@my.linux.server

Then proceed to use winetricks to install dotnet and vcrun2008. X11 is
only needed to install these two libraries, not to run msconvert.

Also, since proteowizard 2.0 release includes thermo's msfilereader
DLL, you do not need to install that either. It was only necessary for
1.x versions. Many thanks to Thermo for supporting the research
community and open source projects like PWIZ!

-angel

On Feb 10, 11:17 am, Angel <delag...@gmail.com> wrote:
> Y, I have wine working with msconvert from proteowizard.
>
> # NOT COVERED: You need to install wine as per you linux distro
> # Then use winetricks to get some deps

> curl -Ohttp://www.kegel.com/wine/winetricks

> chmod 755 winetricks
> ./winetricks winxp
> ./winetricks vcrun2008
> ./winetricks dotnet20
>
> # then get msfilereader from thermo

> curl -Ohttp://sjsupport.thermofinnigan.com/software/msfilereader_ver-13_04-1...

> unzip msfilereader_ver-13_04-14-2009_Setup.zip
> wine msiexec /q  /i /msfilereader_ver-13_04-14-2009_Setup/setup_msi/
> thermo\ install.msi
>
> # then get the latest windows version of pwiz

> curl -L  -o pwiz.ziphttp://sourceforge.net/projects/proteowizard/files/proteowizard/1.6.0...