The following open source components can be used in conjunction with LabKey Server. Some of these components are included in the default LabKey Server installation for Windows. For other platforms, you need to download and compile them yourself. This page lists the licenses that govern their use. If you are not using some modules, you do not need all of these tools.
R
Graphviz (All)
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:
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:
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:
pepmatch (MS1, MS2)
- LabKey Development Owner: jeckels#at#labkey.com
- Windows binary is included with LabKey Server installer.
- Install Instructions:
Credits
See
full credits.