1. How do I configure an Apache server?
2. How do I configure an IIS server? Updated 2004/10/22
3. Tandem seems to run, but my results aren't being created.
4. Why do I get internal server error when I run the search?
5. What's with the CGITemp[12345] files?
6. I get the following error after submitting a tandem web search on Linux:
   "starting thread 1 ... mprocess::spectra failed to open spectrum file : CGItemp63867 mprocess::load failure to load spectra error pProcess->LoadParameters returned error (main)"
7. I get the following error after submitting a tandem web search on Linux:
   "starting thread 1 ...mprocess::load failure to create taxonomy settings error pProcess->LoadParameters returned error (main)"
8. I get the following error in my Apache error log:
   The system cannot find the path specified. : couldn't create child process: 720003: thegpm.pl
   The system cannot find the path specified. : couldn't spawn child process:720003: thegpm.pl
9. Why don't the spectra images appear on the peptide page?
10. How do I add a new search method?

The configuration of the Apache server is controlled by a text file called httpd.conf. On a Linux machine this is most likely found at /etc/httpd/conf/. On a Windows machine it is most likely found at C:/Program Files/Apache Group/Apache(2)/conf/. This file can be editted in any text editor.

The easiest way to configure the Apache server to run GPM, is to change Apache's DocumentRoot directive to "C:/Program Files/Apache Group/Apache2/htdocs/thegpm" on Windows or "/var/www/thegpm/" on Linux. Make the same change to the line about 25 lines down, as follows for Windows:

# This should be changed to whatever you set DocumentRoot to.
#
<Directory "C:/Program Files/Apache Group/Apache2/htdocs/thegpm">
							

or for Linux:

# This should be changed to whatever you set DocumentRoot to.
#
<Directory "/var/www/thegpm">
							

The only other changes required if Apache is set up this way is to add a new ScriptAlias directive as follows for Windows:

ScriptAlias /thegpm-cgi/ "C:/Program Files/Apache Group/Apache2/htdocs/thegpm/thegpm-cgi/"
							

or for Linux:

ScriptAlias /thegpm-cgi/ "/var/www/thegpm/thegpm-cgi/"
							

And set the permissions on thegpm-cgi directory by adding the following for Windows:

<Directory "C:/Program Files/Apache Group/Apache2/htdocs/thegpm/thegpm-cgi">
    AllowOverride None
    Options None
    Order allow,deny
    Allow from all
</Directory>
							

or for Linux:

<Directory "/var/www/thegpm/thegpm-cgi">
    AllowOverride None
    Options None
    Order allow,deny
    Allow from all
</Directory>
							

It is not manditory to configure Apache with the DocumentRoot changed this way, but otherwise a number of Alias directives must be added for folders within thegpm folder. These changes are made in the Alias section of httpd.conf. For example on Windows:

Alias /tandem/ "C:/www/thegpm/tandem/"
<Directory "C:/www/thegpm/tandem">
    Options Indexes MultiViews
    AllowOverride None
    Order allow,deny
    Allow from all
</Directory>
							

or on Linux:

Alias /tandem/ "/pathto/custom/thegpm/tandem/"
<Directory "/pathto/custom/thegpm/tandem">
    Options Indexes MultiViews
    AllowOverride None
    Order allow,deny
    Allow from all
</Directory>
							

Aliases must be added as above for the 'cache', 'gpm' and 'pics' folders as well. Be sure to restart the Apache service after the changes are made. On Windows from the start menu go to Settings/Control Panel/Administrative Tools/Services. On Linux open a command prompt and enter the following command: service httpd restart or /etc/sbin/httpd restart.

Setting up IIS to run thegpm requires that the following virtual directories be created under the default web site: tandem, cache, gpm, pics, thegpm-cgi. To create them, open IIS from the Administrative Tools/Internet Information Services menu item on the start menu. Right click Default Web Site, select New/Virtual Directory. Follow the steps in the dialogs presented.

The only thing to watch is the permissions that you allow. To set permissions, right click on the directory in the IIS tree in the left pane and choose properties. On the Virtual Directory tab, select the properties that apply to that folder. Tandem, cache and gpm directories need read/write allowed. pics only needs read.

thegpm-cgi needs special treatment. It needs to have write permissions and it needs to be able to execute scripts. To set up the script execution permissions, on the Virtual Directories tab, click 'Configuration'. Click 'Add' on the dialog that appears. In the executable text box, type the path to perl or browse to it using the browse button. It is most likely found at 'C:\perl\bin\perl.exe'. After the path, type %s %s, so the final entry should look something like: C:\perl\bin\perl.exe %s %s. In the extension text box enter .pl. Click OK. Click OK again. NOTE: If perl is installed after IIS, this step may not be required.
Still on the Virtual Directory tab, select Scripts only in the Execute Permissions drop down list.

Finally, make sure the user assigned has execute permissions. To see this, select the Directory Security tab. Click Edit button in the Anonymous access section. Click the browse button, click Advanced, click Find now. The list should be populated with all registerd user types on the computer. Select one that has execute permissions. This is where security can be an issue. You may have to create a new user with enough permissions to do this because you don't want to use the Administrator account for this. You may want to take this up with your security people if the site is available outside your lan. If you have a user that fits the bill, select it and click ok. Click ok two more times. After changes are made to the IIS configuration, the site needs to be restarted. Right click Default Web Site, select stop. Repeat and this time select start. This should be all, so point your browser to http://localhost/tandem/thegpm_tandem.html and you should see the search page. Try running a search.

There is a good document here: http://aspn.activestate.com/ASPN/docs/ActivePerl/faq/Windows/ActivePerl- Winfaq6.html that gives some pointers if you run into trouble.

More information on setting up IIS can be found at Microsoft's site.

If you are running a Linux server make sure the permissions for thegpm related folders are set properly. The folder named thegpm-cgi must allow for read/write/execute and the following directories must allow for read/write access: /thegpm/cache, /tandem/archive, tandem/archive/pics.

An internal server error can be caused by any number of configuration or script errors.

• If you are running a Windows server, make sure that you have perl installed. If not, download an install ActiveState Perl. Linux usually has a version of Perl already, although you may need to get a more complete version of CGI.pm.
• Make sure the first line in all the perl script files(.pl) have the correct path to the perl executable on the server.
• If you are running on a Linux server, make sure the the perl scripts have executable permissions.

These are the spectra files from the upload. If you are running on Windows, perl uploads files to C:/Temp if it exists or the current directory (xml-cgi) if it doesn't. These files should be automatically deleted by perl, but often on Windows, they are not. Make sure the folder allows for read/write access.

The GPM uploads the spectra file to /usr/tmp or the /tmp directory on Linux. Make sure the appropriate folder allows for read/write access.

This error is most likely caused by an incorrect path in the taxonomy.xml file. This file can be found in the tandem folder. The URL paths in this file must point to the location of your local fasta files.

This error is caused by not having the correct path to perl in the first line of all the perl script files(.pl). Make sure this path points to the correct location of the perl executable on the server.

The spectra images are created using an XML language called SVG (Scalable Vector Graphics). In order to view these images, your browser must have the Adobe SVG plug-in installed. It can be downloaded here.

To create new methods or edit existing methods, open one of the .xml files in the /tandem/methods folder (eg: qstar.xml) and follow that format. Or, simply copy the entire contents into a new empty file and make the changes to the new file, saving it with a name that gives some hint as to what type of search it describes and an xml extension. There are descriptions provided for what each parameter does in the xml file.

In order to have the new method appear in the select list, it needs to be added the the file named thegpm_tandem.html found in the /tandem directory. Open the file in a text editor and find the line that looks like this:

<select size="4" class="small_value" name="lpdp" ID="Select1">
							

Directly below this line are the options that show up in the select list. Copy & paste an existing line to the end of the options list. Change the value parameter of the option tag to reflect the name of the new xml method file. Change the text that appears between the > and the </option> to something that describes your newly created method. For example:

<option value="/tandem/methods/iontrap.xml">Ion Trap (4 Da)</option>
<option value="/tandem/methods/newmethod.xml">New method (30 ppm)</option>