Hello,

We don't distribute the native Linux binaries for pwiz or other third-party tools in either SVN or our .tar.gz distributions. You'll need to grab the ProteoWizard binaries directly from their site:

http://proteowizard.sourceforge.net/downloads.shtml

You'll need to put the binaries on your LD_LIBRARY_PATH (an environment variable) or point the JVM to them using a -Djava.library.path argument at Tomcat startup time.

Additionally, you'll need to add/enable a line in your labkey.xml or equivalent file as documented here:

https://www.labkey.org/wiki/home/Documentation/page.view?name=WorkingWithmzML

Thanks,
Josh

Hi Josh,

I did install Proteowizard under /users/local/pwiz from the tar.bz2 file from souceforge, but do not see a pwiz_swigbindings file in this folder. Does Proteowizard have to be installed from source? The other problem I encountered was, that in Ubuntu 10.04 it seems to be difficult to set LD_LIBRARY_PATH, could you give me more specific instructions how to set a -Djava.library.path argument instead?

Thanks a lot,

Maik

Maik,

With respect to the library path question

I am not sure how you are starting your tomcat server. In your tomcat startup script you add the following to either the JAVA_OPTS or CATALINA_OPTS variable

-Djava.library.path=/path/to/library


With respect to the pwiz_swigbindings library:

It looks like you can build the library from source via the TPP version 4.4.0 or later. You can use the make command described in our documentation, ie "...The pwiz_swigbindings library can be built using the TransProteomic Pipeline build system ("make pwiz_swig"), and will be added to the standard ProteoWizard build soon as well, hopefully."

I have not tried myself on Ubuntu yet, thus I cannot verify that this make command will work.