R

• Website: http://www.r-project.org/
• LabKey Development Owner: jeckels#at#labkey.com
• Install Instructions: Install and Set Up R.
• License: GNU GPL 2.0

Graphviz (All)

• Component Name: Graphviz
• LabKey Development Owner: jeckels#at#labkey.com
• Install Instructions: http://www.graphviz.org/Download.php.
• Build instructions:
• For current version, use the INSTALL link here: http://www.graphviz.org/doc/build.html
• Ensure that the location of dot.exe is on your server path (i.e., the path of the user running the Tomcat server process).
• Alternative:
• Sun also ships an old version with Solaris (http://www.sun.com/software/solaris/freeware/), although we have not tested LabKey Server with that version.
• License: Common Public License

Trans Proteomic Pipeline (MS2)

• LabKey Development Owner: jeckels#at#labkey.com
• 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://sashimi.svn.sourceforge.net/svnroot/sashimi/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 Mac OSX, this software is only supported for Macs running on Intel CPUs.
• If you wish to use TPP version 4.3.1 to produce comparable results to previous datasets, follow these instructions for getting the source instead:
• Download Location: http://sourceforge.net/project/showfiles.php?group_id=69281&package_id=126912
• Download v4.3.1 of the tools and unzip or obtain directly from Subversion at https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-1.
• Apply the attached patch file.
• If you experience a problem applying the patch using your subversion client, then use the attached zip file. The file structure of the zip file matches the directory structure of the source files.

X!Tandem (MS2)

• Component Name: X!Tandem
• LabKey Development Owner: jeckels#at#labkey.com
• Information: As of version 9.3, LabKey Server uses a version of X!Tandem that is included with the TPP.

Proteowizard (MS1, MS2)

• LabKey Development Owner: jeckels#at#labkey.com
• Information on ProteoWizard: http://proteowizard.sourceforge.net/
• Windows binary is included with LabKey Server installer.
• 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.

peakaboo (MS1)

• LabKey Development Owner: jeckels#at#labkey.com
• Information on ProteoWizard: http://proteowizard.sourceforge.net/
• Windows binary is included with LabKey Server installer.
• Install Instructions:
• Download Location: http://proteowizard.sourceforge.net/download.html
• Download source or binaries as appropriate for your platform.
• If downloading source, build as appropriate for your platform.
• Copy to your pipeline tools directory.

pepmatch (MS1, MS2)

• LabKey Development Owner: jeckels#at#labkey.com
• Windows binary is included with LabKey Server installer.
• Install Instructions:
• Download source code: pepmatch.tar.gz (zipfile) or
• Check out source code using Subversion. https://hedgehog.fhcrc.org/tor/stedi/trunk/tools/pepmatch
• username = cpas
• password = cpas
• Run "make" to build.
• Copy pepmatch binary to your pipeline tools directory.

Credits