LabKey makes available pre-built Windows binaries of various proteomics analysis tools, including executables such as X!Tandem, Comet, the Trans-Proteomic Pipeline, msInspect, and Proteowizard. This step is optional, a convenience for users and developers who are interested in developing proteomics functionality and/or running proteomics-related tests. TeamCity, LabKey's automated build and test system, is configured to automatically grab these tools as part of its normal build and test process.
These tools are available in a special location on the standard SVN server. For those who will be developing and testing proteomics-related functionality on Windows, we recommend checking out the current versions into a standard LabKey Server enlistment using the following commands (the same can be accomplished using TortoiseSVN or other tools) from your %LABKEY_ROOT%/external/windows directory:
svn co https://hedgehog.fhcrc.org/tor/stedi/binaries/proteomics/comet
svn co https://hedgehog.fhcrc.org/tor/stedi/binaries/proteomics/labkey
svn co https://hedgehog.fhcrc.org/tor/stedi/binaries/proteomics/msinspect
svn co https://hedgehog.fhcrc.org/tor/stedi/binaries/proteomics/pwiz
svn co https://hedgehog.fhcrc.org/tor/stedi/binaries/proteomics/tpp
This will create separate subdirectories for each set of tools. Invoking "gradlew deployApp" will deploy the binaries into the standard %LABKEY_ROOT%/build/deploy/bin directory, where they will be available for usage.