Configure Mascot Support

If you are not familiar with your organization's Mascot installation, you will want to recruit the assistance of your Mascot administrator.

Before you configure Mascot support, have the following information ready:

  • Mascot Server Name: Typically of the form mascot.server.org
  • User: The user id for logging in to your Mascot server (leave blank if your Mascot server does not have security configured)
  • Password: The password to authenticate you to your Mascot server (leave blank if your Mascot server does not have security configured)
  • HTTP Proxy URL: Typically of the form http://proxyservername.domain.org:8080/ (leave blank if you are not using a proxy server).

Enter this information in the site-wide or project/folder specific Mascot settings, as described below.

Site-Wide Configuration

To configure Mascot support across all projects on the site:

  • Select Admin > Admin Console
  • In the Configuration section, click the Mascot Server link.
  • Specify the Mascot server name, the user name and password used to authenticate against the Mascot server, if Mascot security is enabled. Optionally, specify the HTTP Proxy URL, if your network setup requires it.

Project and Folder Specific Configuration

You configure Mascot support for a specific project or folder that overrides any site-wide configuration.  To configure project or folder specific Mascot support:

  • Create or navigate to project or folder of type MS2
  • In the Data Pipeline web part, click Setup.  
  • Click Configure Mascot Server.
  • By default, the project/folder will inherit the Mascot settings from the site-wide configuration. To override these settings for this project/folder, specify the Mascot server name, the user name and password used to authenticate against the Mascot server, if Mascot security is enabled. Optionally, specify the HTTP Proxy URL, if your network setup requires it.

Test the Mascot Configuration

To test your Mascot support configuration, select Admin > Admin Console, then click the Mascot Server link. Click Test Mascot Settings. A window will open to report the status of the testing.

If the test is successful, LabKey displays a message indicating success and displaying the settings used and the Mascot server configuration file (mascot.dat).

If the test fails, LabKey displays an error message, followed by one of the following additional messages to help you troubleshoot.

  • is not a valid user: Check that you have entered the correct user account. Contact your Mascot administrator for help if problem persists.
  • You have entered an invalid password: Check that you have entered the right password. Ensure that your CAPS lock and NUM lock settings are correct. Contact your Mascot administrator for help if problem persists.
  • Failure to interact with Mascot Server: LabKey cannot contact the Mascot server. Please check that the Mascot server is online and that your network is working.

Set Up Sequence Database Synchronization

The Perl script labkeydbmgmt.pl supports the download of sequence database from your Mascot server. To download the Perl script, click: here The database is needed to translate the Mascot result (.dat file) to pepXML (.pep.xml file).

  1. Copy the Perl script labkeydbmgmt.pl to the folder /cgi/.
  2. Open labkeydbmgmt.pl in a text editor and change the first line to refer to your Perl executable full path. (See your copy of /cgi/search_form.pl for the correct path.)
  3. If your Mascot runs on a *nix system, you need to set the execution attribute. (Command: chmod a+rx labkeydbmgmt.pl).

Supported and Tested Mascot Versions

To get your Mascot server version number check with your Mascot administrator. You can use the helper application at /bin/ms-searchcontrol.exe to determine your version. Usage: ./ms-searchcontrol.exe –version.

If your Mascot Server version is v2.1.03 or later, LabKey should support it with no additional requirements. If your Mascot Server version is v2.0.x or v2.1.x (earlier than v2.1.03), you must perform the following upgrade: - Visit the Matrix Science website for the free upgrade (http://www.matrixscience.com/distiller_support.html#CLIENT). - Ask your Mascot administrator to determine the correct platform upgrade file to use and to perform the upgrade. Remember to back up all files that are to be upgraded beforehand. - As the Mascot result is retrieved via the MIME format, you must make the following highlighted changes to client.pl:

140: close(SOCK);
141: print @temp;
142:
143:# WCH: 28 July 2006
# Added to support the retrieval of Mascot .dat result file in MIME format
# This is necessary if you are using Mascot version 2.0 or 2.1.x (< v 2.1.03) and
# have upgraded to the version 2.1 Mascot daemon
} elsif (defined($thisScript->param('results'))
|| defined($thisScript->param('xmlresults'))
|| defined($thisScript->param('result_file_mime'))) {
# END - WCH: 28 July 2006

144:
145: if ($taskID < 1) {
146: print "problem=Invalid task ID - $taskID\n";
147: exit 1;
148: }
149:
150: # Same code for results and xmlresults except that the latter requires
151: # reporttop and different command to be passed to ms-searchcontrol
152: my ($cmnd, $reporttop);
153: if (defined($thisScript->param('xmlresults'))) {
154: $cmnd = "--xmlresults";
155: if (!defined($thisScript->param('reporttop'))) {
156: print "problem=Invalid reporttop\n";
157: exit 1;
158: } else {
159: $reporttop = "--reporttop " . $thisScript->param('reporttop');
160: }
# WCH: 28 July 2006
# Added to support the retrieval of Mascot .dat result file in MIME format
# This is necessary if you are using v2.0 Mascot Server and
# have upgraded to the version 2.1 Mascot Daemon
} elsif (defined($thisScript->param('result_file_mime'))) {
$cmnd = "--result_file_mime";
# END - WCH: 28 July 2006

161: } else {
162: $cmnd = "--results";
163: }
164:
165: # Call ms-searchcontrol.exe to output search results to STDOUT

Note: LabKey has not been tested against Mascot version 1.9.x or earlier. Versions earlier than 1.9.x are not supported or guaranteed to work. If you are interested in using an earlier version, you will need commercial-level support.  This level of assistance is available from the LabKey technical services team. Please contact LabKey.

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