This topic covers third-party components which are often used in conjunction with LabKey Server to enhance its functionality. All of these components are optional and are not required for the server to work in general, but some are required for specific use cases.

• R
• Graphviz
• Trans Proteomic Pipeline and X!Tandem (MS2)
• Proteowizard (MS2)

R

Website: http://www.r-project.org/

Install Instructions: Install and Set Up R.

License: GNU GPL 2.0

Graphviz (All)

Component Name: Graphviz

Download: https://graphviz.gitlab.io/download/

Documentation: https://graphviz.gitlab.io/documentation/

License: Common Public License

Trans Proteomic Pipeline and X!Tandem (MS2)

Information on TPP: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP

LabKey Server uses a version of X!Tandem that is included with the Trans Proteomic Pipeline (TPP).

If you are using XPRESS for quantitation as part of your analysis, you will also need to have Perl installed and available on your path.

Install Instructions:

• Download pre-built binaries
• Linux
• OSX
• Windows
• Build from Source
• Download the source distribution of v4.6.3 of the tools and unzip or obtain directly from Subversion at https://svn.code.sf.net/p/sashimi/code/tags/release_4-6-3.
• Build the tools
• Edit trans_proteomic_pipeline/src/Makefile.incl
• Add a line with XML_ONLY=1
• Modify TPP_ROOT to point to the location you intend to install the binaries. NOTE: This location must be on your server path (ie the path of the user running the Tomcat server process).
• Run 'make configure all install' from trans_proteomic_pipeline/src
• Copy the binaries to the directory you specified in TPP_ROOT above.

License: LGPL

Proteowizard (MS2)

Information on ProteoWizard: http://proteowizard.sourceforge.net/

Install Instructions:

• Download Location: http://proteowizard.sourceforge.net/downloads.shtml
• Download source or binaries as appropriate for your platform.
• If downloading source, build as appropriate for your platform.
• Copy to your pipeline tools directory.

Installation Checklist

1. Install on Linux: Main Components OR Install on Windows: Main Components
2. Installation: Tomcat Configuration
3. Installation: SMTP, Encryption, LDAP, and File Roots
4. (Current Topic) Third-Party Components and Licenses