TPP:Windows Cygwin Installation

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-== Example Data Analysis == 
-=== Windows / Cygwin Example === 
-==== Sequest Searched Data Example ==== 
-===== Getting Example Data ===== 
-# Make sure you have at least <b>1 Gig</b> of space on your harddrive before you start! 
-# Download the file from the following link: http://tools.proteomecenter.org/sample_data/raftapr_searched.tgz 
-## Save the file in the <b>c:\Inetpub\wwwroot\ISB\data</b> directory on your computer 
-## Using WinZip or a similar application extract all of the files in the compressed archive file to the current directory. 
-## After extraction you should have a directory <b>c:\Inetpub\wwwroot\ISB\data\raft</b> that contains many files. 
-===== Converting Searched Data to pepXML =====+==Next Steps==
-The sample data you've [[TPP:User_Documentation#Getting_Example_Data|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.+===[[TPP:Using Petunia|Using the TPP web interface ("Petunia")]]===
-# Open and log into the [[TPP:User_Documentation#Accessing_Petunia_.28Windows_.2F_Cygwin.29|TPP Web Interface]].+
-# On the '''Home''' tab make sure that the ''Sequest'' analysis pipeline is selected.+
-## Click on the '''ANALYSIS PIPELINE''' 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]]+
-## 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.+
-# In the second pane, ''"Specify Sequest Parameters File"'', click on the ''"Add Files"'' button+
-## 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.+
-# 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;"/>+
-==== Additional Sample Data Sources ====+===[[TPP:Example data analysis|Example Data Analysis]]===
-* 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+

Revision as of 23:53, 9 April 2007

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


Next Steps

Using the TPP web interface ("Petunia")

Example Data Analysis

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