As of version 13.3, the standard Subversion repository for LabKey Server no longer includes the pre-built binaries of the proteomics analysis tools for Windows. This includes executables such as X!Tandem, Comet, the Trans-Proteomic Pipeline, msInspect, and Proteowizard. This is due to the increasing size of some of these tools, and an acknowledgement that not all LabKey Server developers and users are interested in doing proteomics analysis.
This step is optional, and will not affect users or developers who are not 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.
Instead, updated versions of the tools have been moved to a separate location in the same 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 (this 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. Doing a "gradlew deployApp" will deploy the binaries into the standard %LABKEY_ROOT%/build/deploy/bin directory, where they will be available for usage.