TPP:5.1 Installation

TPP 5.1 (Syzygy) is the latest release of the popular proteomics analysis pipeline. More information can be found here: TPP:5.1.0_Release_Notes.

New Windows install

This assumes that you do not have a previous version of TPP installed on your system.

As of version 5.0.0, no dependencies are required to install TPP on a modern Windows system. A customized version of the Perl language and the Apache web server are included and installed by default; users can choose to use other versions, but this has not been fully tested and may lead to unstable behavior.

• Download the latest version of the TPP installer for Windows and run it.

• After you accept the license agreement, you will be asked to select a location to install TPP and its components. The default is C:\TPP\, but can be changed to any other location.

• You will then be asked to select a web server port number for TPP to use. The default value 10401 should work fine in most cases. You can enter any other legal port number instead.

 Do note that this will make all links in TPP look like this:
   http://www.myhost.org:10401/tpp/cgi-bin/tpp_gui.pl

• You will then be asked to select the location of your data, which can be on the local drive or an external drive. A few example locations:
  • Local drive data installation (default for new installations): C:\TPP\data\
  • Use old TPP data location: C:\Inetpub\wwwroot\ISB\data\
  • Data on another drive, e.g.: E:\data\proteomics\

• Lastly, you will be asked to choose which extra components to install:
  • Apache web server: needed for graphical user interfaces. May not need if you already have another server installed and running, or are not using TPP interfaces.
  • ProteoWizard: needed for RAW->mzML file conversions; includes 3rd party vendor libraries and special licenses. Please make yourself familiar with these if you choose to install this component.
  • Download and install dependencies for ProteoWizard: automatically install required components. If left out, you may need to update your system to perform certain file conversions.
  • Strawberry Perl: Custom distribution of the Perl language; *strongly* recommended. You may omit and try to use your own installation of Perl, but this is not well tested and may lead to unstable behavior.

• Reboot when prompted.

TPP Tray

TPP now includes a convenient 'tray' application (TPP Tray). It provides quick access to start/stop the TPP web server, as well as links to the Petunia interface, data folder, TPP version, server status, among others. This is not started by default, so you will need to open a command window ("cmd") and type: tpptray if you wish to use this feature.

Since TPP Tray needs to run as Administrator, you may be asked to provide admin credentials for it to run -- upon initial invocation and upon system startup. The TPP Tray is optional, and not needed for TPP to operate. If you do not have admin access to your machine, or do not wish to provide these credentials, simply close the prompt window and continue.

If you wish to disable TPP Tray upon system startup, please follow the instructions in this page (look for TPP Tray and unclick it): http://www.howtogeek.com/74523/how-to-disable-startup-programs-in-windows/

Should you wish to run it later, just open a command window ("cmd") and type: tpptray.

Upgrading from 5.0.0 on Windows

Before running the installer, please make sure that the TPP web server (if using one) is not running.

• You can most easily check the status by clicking on the TPP Tray; click on Stop TPP web server if it shows that it is running.
• If TPP Tray is not running, open the Windows Task Manager, click on the Services tab, and look for TPPApacheWebService. Right-click on this item and select to Stop Service.

Continue the steps for a new installation (above), making sure that the data location and port values are correct; adjust if necessary.

Upgrading from 4.8.x on Windows

For best results, it is strongly recommended that you uninstall TPP, ActiveState perl, and the Apache web server -- unless you are using either of the last two components for other purposes. Once you have done this, please follow the steps described above for a new Windows install; pay close attention to the location of the data directory, as you may choose to use the location of your existing data for easy transition to the new TPP.

In some systems it might be sufficient to simply uninstall ActiveState Perl and then install TPP 5.1, but this has not been observed to work for all users. If you try this and it fails, consider following the instructions for a new installation as described above.

Installing on Linux

Please follow the instructions included in the BUILD_LINUX file found at the top-level of the distribution.

We also have recipes for building TPP in various Linux distributions.

Installing on OSX

As of this writing, we do not provide explicit support for OSX. Please share your experience with us if you are able to install it. We otherwise plan on providing this in the near future.