TPP:Windows Cygwin Installation

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Windows Installation

* These instructions are meant for the installation of the Cygwin-based TPP, which is now obsolete.

* Please follow the steps here and in the installation wizard instead.


This installation will install a Unix environment (Cygwin) on your Windows system. The installation process is automated and not complicated. If you use BioworksBrowser and SequestBrowser, please download and install these tools prior to installing the SPC software. By default the software installs and uses the Apache2 webserver. The Apache2 webserver is configured to answer only on port 1441, so it should not conflict with an existing instance of IIS (the default Windows webserver).

Downloading and Running the Setup.exe Installation Program

  1. You must be logged on as an Administrator to install these tools.
  2. Make sure that all Windows operating system updates have been installed!
  3. Download the TPP_Cygwin_Setup.exe installation program. Note, you'll only need to download this once. When we release new versions you can still use the same installer.
  4. Follow default installation by clicking "Next" at each installation step, until the installation is completed. Please note: cygwin installation directory must be C:\cygwin
  5. Reboot the computer
  6. If everything worked correctly you should be able to now access the TPP web interface

Setup.exe Installation Walkthrough

Starting/Stopping Apache

Note: It is usually not necessary manually start the webserver if the computer was rebooted after installation. Only do this step if there is a problem with the webserver startup.

  • Open Control Panel → Administrative Tools → Services
  • Start the service cygapache2_stop to STOP Apache2 for cygwin
  • Start the service cygapache2_start to START Apache2 for cygwin
  • Please allow up to a minute for each service to do its job, these services will finish automatically

Installation Troubleshooting

  • Reboot the computer. System environmental variables are not reset until this step occurs!
  • Make sure that all Windows updates have been installed!
  • Open Control Panel → System → Advanced → Environment Variables and verify that the following System variables are set:
Set to "C:\Inetpub\wwwroot\"
Set to "http://localhost:1441/"
Set to "C:\Inetpub\tpp-bin\cometlinks.def"
Begins with "C:\cygwin\usr\X11R6\bin;C:\cygwin\bin;"
  • Open Control Panel → Administrative Tools → Services and verify that the following Services are present:
Startup Type set to Automatic
Startup Type set to Automatic
Startup Type set to Manual

ADVANCED apache2/cygwin debugging

If you try "http://localhost:1441" and cannot connect to the server, and you have manually tried restarting starting services from the Services control panel:

  1. stop and disable services from Services control panel
  2. close all cygwin windows
  3. Start->Run : "C:\cygwin\bin\bash.exe" to get a new shell
  4. in this shell: first try to start the servers manually:
  5. /usr/sbin/cygserver & -- look for any error messages, should be none unless cygserver is already running, which is ok.
  6. CYGWIN=server /usr/sbin/apachectl2 -k start -- look for any error messages, should be none
  7. if error messages from the last two steps that includes "couldn't remap" or "died waiting for DLL loading", proceed with the following steps (following this link):
    1. close all cygwin windows
    2. Start->Run : "C:\cygwin\bin\ash.exe" to get a simple shell; the following command can only be run from within ash, NOT bash
    3. /bin/rebaseall
    4. try to manually start cygwin servers again

Reininstalling the TPP Software

If you are upgrading, you don't have to do anything special. Note, you do not have to re-download the cygwin setup program; re-running will find the latest version via the internet. Just follow the Cygwin installation instructions listed above.

Clean Install

If you encountered a problem, you can do a "clean install" by following the uninstall instructions and then trying the Cygwin installation instructions listed above.

Forcing Reinstall

If you want to force the current version to reinstall, rerun the cygwin installer. When you get to step 6 (in install screenshot section above), expand the "base" section, find the first entry "ISB-MS-Tools", click on "keep" until it changes to reinstall, and proceed.

Uninstalling the TPP

Occasionally it will be necessary to uninstall the software, for example, in the case of an incomplete or broken installation.

  1. close all cygwin windows
  2. exit the cygwin X server if you have started it (right click on the "X" in the bottom right toolbar if it is there and choose "exit")
  3. Stop cygwin services. Note, these may not exist if installation failed. Open Control Panel → Administrative Tools → Services, start "cygapache2_stop" (if it exists), then set all cygapache2 and cygserver services to "disabled"
  4. delete the C:\cygwin directory. If you get the warning that files are in use and cannot be deleted, log off and/or restart your machine, then try again.
  5. remove shortcuts from the Start Menu (right-click on the "TPP" group and delete.)
  6. back up any custom programs or scripts and delete the C:\Inetpub\tpp-bin directory.

(OPTIONAL!) Running with the IIS webserver instead of Apache

Older installations of the TPP used the Microsoft IIS webserver. While it is possible to install under this configuration, we no longer recommend or support it. The cygwin installation now installs it's own webserver, Apache 2, on port 1441.

Old, out-of-date, unsupported IIS configuration instructions can be found here.

Next Steps

Using the TPP web interface ("Petunia")

Example Data Analysis


original author: David Shteynberg

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