TPP:Windows Cygwin Installation

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===== Analyzing Example Data ===== ===== Analyzing Example Data =====
# Open and log into the [[TPP:User_Documentation#Accessing_Petunia_.28Windows_.2F_Cygwin.29|TPP Web Interface]]. # Open and log into the [[TPP:User_Documentation#Accessing_Petunia_.28Windows_.2F_Cygwin.29|TPP Web Interface]].
-# The sample data you've [[TPP:User_Documentation#Downloading_Example_Data|Downloaded]] was searched with '''Sequest''' using the ''runsearch'' tool. This tools generated an HTML summary for every MS run (mzXML) file that was searched.+# The sample data you've [[TPP:User_Documentation#Getting_Example_Data|Downloaded]] was searched with '''Sequest''' using the ''runsearch'' tool. This tools generated an HTML summary for every MS run (mzXML) file that was searched.
==== Additional Sample Data Sources ==== ==== Additional Sample Data Sources ====

Revision as of 23:59, 2 November 2006

Contents

Installation

Windows / Cygwin Installation

Setup.exe Installation Program

  1. You must be logged on as an Administrator to install these tools.
  2. Download the setup.exe installation program from this link http://tools.proteomecenter.org/software/cygwin/setup.exe
  3. Follow default installation by clicking "Next" at each installation step, until the installation is completed
  4. Reboot the computer
  5. If everything worked correctly you should be able to now access the TPP Web Interface

Setup.exe Installation Gallery

1. Select to
"Install from the Internet"

2. The default installation will install cygwin to c:\cygwin.
Keep the other options set to default "RECOMMENDED" settings.

3. Select a directory where you want to download the temporary
installation files. If unsure the "Desktop" is a good default.

4. Choose "Direct Connection" to the Internet.

5. Select "http://tools.proteomecenter.org" as the Download Site.

6. All default installation packages should be installed
along with any automatically selected dependencies.

Starting/Stopping Apache

  • 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

  • Open Control Panel → System → Advanced → Environment Variables and verify that the following System variables are set:
WEBSERVER_ROOT
Set to "C:\Inetpub\wwwroot\"
WEBSERVER_URL
Set to "http://localhost:1441/"
COMETLINKSFILE
Set to "C:\Inetpub\tpp-bin\cometlinks.def"
PATH
Begins with "C:\cygwin\usr\X11R6\bin;C:\cygwin\bin;"
  • Open Control Panel → Administrative Tools → Services and verify that the following Services are present:
cygserver
Startup Type set to Automatic
cygapache2_start
Startup Type set to Automatic
cygapache2_stop
Startup Type set to Manual

Using Petunia 

Petunia is the name for the Web Interface for interacting with the TPP tools.

Accessing Petunia (Windows / Cygwin)

  • To access Petunia open a Web Browser and refer it http://localhost:1441/tpp-bin/tpp_gui.pl
    • If you have a Petunia icon entitled TPP Web Tools on the Desktop you can access the interface by clicking on the icon.
    • You may also find Petunia in Start → Program Files → TPP → TPP Web Tools.
Enlarge
  • You should be presented with a Login page asking for a user name and password. The default login authentication: Username: guest, Password: guest


Enlarge
  • If login was successful the next page will be a Welcome page.


Example Data Analysis

Windows / Cygwin Example

Sequest Searched Data Example

Getting Example Data
  1. Make sure you have at least 1 Gig of space on your harddrive before you start!
  2. Download the file from the following link: http://tools.proteomecenter.org/sample_data/raftapr_searched.tgz
    1. Save the file in the c:\Inetpub\wwwroot\ISB\data directory on your computer
    2. Using WinZip or a similar application extract all of the files in the compressed archive file to the current directory.
    3. After extraction you should have a directory c:\Inetpub\wwwroot\ISB\data\raft that contains many files.
Analyzing Example Data
  1. Open and log into the TPP Web Interface.
  2. The sample data you've Downloaded was searched with Sequest using the runsearch tool. This tools generated an HTML summary for every MS run (mzXML) file that was searched.

Additional Sample Data Sources

Retrieved from "http://tools.proteomecenter.org/wiki/index.php?title=TPP:Windows_Cygwin_Installation"
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