If you are using the MS2 module, you may need to install the following:

Trans Proteomic Pipeline and X!Tandem

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).
    • Run 'make configure all install' from trans_proteomic_pipeline/src
    • Copy the binaries to the directory you specified in TPP_ROOT above.
License: LGPL

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