TPP:Windows Cygwin Installation

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	## Click on the '''ANALYSIS PIPELINE''' tab.		## Click on the '''ANALYSIS PIPELINE''' tab.
	## Click on the '''pepXML''' tab.		## Click on the '''pepXML''' tab.
-	# In the first pane ''"File(s) to convert to pepXML"'' click on the ''"Add Files"'' button.[[Image:Petunia_raft.jpg|thumb|right]]	+	# In the first pane, ''"File(s) to convert to pepXML"'', click on the ''"Add Files"'' button.[[Image:Petunia_raft.jpg|thumb|right]]
	## Switch to the ''raft'' directory where you extracted the sample data.		## Switch to the ''raft'' directory where you extracted the sample data.
	## Select all HTML files in this directory and click on the '''Select''' button at the bottom of the page when ready.		## Select all HTML files in this directory and click on the '''Select''' button at the bottom of the page when ready.
-	# In the second pane ''"Specify Sequest Parameters File"'' click on the ''"Add Files"'' button	+	# In the second pane, ''"Specify Sequest Parameters File"'', click on the ''"Add Files"'' button
-	## Switch to the ''raft'' directory where you extracted the sample data.	+	## Make sure you are still in the ''raft'' directory where you extracted the sample data.
	## Select the ''sequest.params'' file in this directory and click on the '''Select''' button at the bottom of the page.		## Select the ''sequest.params'' file in this directory and click on the '''Select''' button at the bottom of the page.
		+	# Leave all settings in the third pane, ''"Options"'', unchanged.
		+	# Click on the '''Convert to PepXML''' button in the fourth pane, ''"Convert!"''.
		+	## Wait for the conversions to finish running.
	<br style="clear:both;"/>		<br style="clear:both;"/>

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Revision as of 00:41, 3 November 2006

Contents 1 Installation 1.1 Windows / Cygwin Installation 1.1.1 Setup.exe Installation Program 1.1.2 Setup.exe Installation Gallery 1.1.3 Starting/Stopping Apache 1.1.4 Installation Troubleshooting 2 Using Petunia 2.1 Accessing Petunia (Windows / Cygwin) 3 Example Data Analysis 3.1 Windows / Cygwin Example 3.1.1 Sequest Searched Data Example 3.1.1.1 Getting Example Data 3.1.1.2 Converting Searched Data to pepXML 3.1.2 Additional Sample Data Sources

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.

• You should be presented with a Login page asking for a user name and password. The default login authentication: Username: guest, Password: guest
  • If you have any problems at this point, you may want to consult the Troubleshooting Guide.

• 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.

Converting Searched Data to pepXML

The sample data you've downloaded was searched with Sequest using the runsearch tool. The runsearch tool generates an HTML summary for every MS run (mzXML) file that is searched. The HTML search results must first be converted to pepXML format for further analysis with the TPP.

1. Open and log into the TPP Web Interface.
2. On the Home tab make sure that the Sequest analysis pipeline is selected.
   1. Click on the ANALYSIS PIPELINE tab.
   2. Click on the pepXML tab.
3. In the first pane, "File(s) to convert to pepXML", click on the "Add Files" button.
   

   
   1. Switch to the raft directory where you extracted the sample data.
   2. Select all HTML files in this directory and click on the Select button at the bottom of the page when ready.
4. In the second pane, "Specify Sequest Parameters File", click on the "Add Files" button
   1. Make sure you are still in the raft directory where you extracted the sample data.
   2. Select the sequest.params file in this directory and click on the Select button at the bottom of the page.
5. Leave all settings in the third pane, "Options", unchanged.
6. Click on the Convert to PepXML button in the fourth pane, "Convert!".
   1. Wait for the conversions to finish running.

Additional Sample Data Sources

• Example data is available from many locations including:
  • http://tools.proteomecenter.org/data.php
  • http://www.peptideatlas.org/repository/
  • http://sashimi.sourceforge.net/repository.html