Install Third Party Components: /Documentation

Install Third Party Components

Documentation

Install Third Party Components

This topic covers third-party components which can be used in conjunction with LabKey Server to enhance its functionality. All of these components are optional and only required for specific use cases.

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

R

Install and Set Up R

Graphviz

Install Graphviz

Premium Resource - This is a legacy feature available with Premium Editions of LabKey Server. Learn more or contact LabKey.

Trans Proteomic Pipeline and X!Tandem

If you are using the MS2 module, you may need to install these components.

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 proteomics binaries

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 (i.e. the path of the user running the Tomcat server process).