These components are often used in conjunction with LabKey Server to enhance its functionality. All of the components are optional and are not required for the server to work in general, but some of these components are required for specfic use cases.

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 (MS2)

• Information on TPP: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
• Install Instructions:
• 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
• Notes:
• For OSX, this software is only supported for machines running on Intel CPUs.

X!Tandem (MS2)

• Component Name: X!Tandem
• Information: As of version 9.3, LabKey Server uses a version of X!Tandem that is included with the TPP.

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.