TPP:Using Petunia

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1 First Step
- 1.1 Installing the TPP on Windows
2 Customizing Petunia
- 2.1 How to create a new account
- 2.2 How to change the location of the data files
3 Using Petunia
- 3.1 Accessing Petunia (Windows / Cygwin)
4 Next Step
- 4.1 Example Data Analysis
5 Author

First Step

Installing the TPP on Windows

Customizing Petunia

How to create a new account

Using Windows File Explorer (i.e. My Computer...), navigate to the location of the installation of the TPP tools, typically this is under C:\Inetpub\tpp-bin\.
Locate the users folder, and navigate into it.
On a new installation, you should see one directory, guest. This contains data for that account.
Make a copy of this folder (i.e. 'Copy of guest'), and rename this new folder to whatever you want the new username to be. Make sure you do not use spaces or other non-standard characters.
The new account is now ready; log in through Petunia with the 'guest' password.
Once you log in, go to the Manage My Account tab in Petunia to change the password!.

How to change the location of the data files

Note: if using a removable or network drive, you will need to ensure that the drive is always mounted as the same letter.

First, make sure that the Apache webserver is able to serve content from the new data folder.
- Find the httpd.conf file; typically under C:\cygwin\etc\apache2\
- Make a copy of this file and keep it as a backup, in case you need to revert to it.
- Open the file in your favorite text editor (i.e. Wordpad), and scroll to near the end.
  - Find the line that reads <Directory "/cygdrive/c/Inetpub/wwwroot/ISB/">.
    - Copy and paste all text starting on this line, down to and including the first line that only contains </Directory>.
    - On the newly-pasted block of text, change the directory location within the <Directory...> tag to the new data location:
    - Please note that this has to follow the cygwin-style path. For example, if your data is under E:\Proteomics\Data\TPP_data\, you would change the Directory line to read: <Directory "/cygdrive/e/Proteomics/Data/TPP_data/">. (Note the forward slashes and case-sensitivity)
  - Find the line that reads SetEnv WEBSERVER_ROOT /cygdrive/c/Inetpub/wwwroot/.
    - Change the directory location as above.
- Save the modified file, and restart Apache for the changes to take effect.
Second, modify the Petunia code to point to the new data location:
- You can usually find the Petunia code under C:\Inetpub\tpp-bin\tpp_gui.pl.
- Open this file with your favorite text editor, and modify the following 2 lines:

my $www_root    = "/cygdrive/c/Inetpub/wwwroot/";  # full path to web server root
my $data_dir    = "${www_root}ISB/data/";          # full path to data directory top-level

to reflect the new location. For example:

my $www_root    = "/cygdrive/e/Proteomics/";       # full path to web server root
my $data_dir    = "${www_root}Data/TPP_data/";     # full path to data directory top-level

Save this file, and log into Petunia.

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.