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:
Enter this information in the site-wide or project/folder specific Mascot settings, as described below.
To configure Mascot support across all projects on the site:
You configure Mascot support for a specific project or folder that overrides any site-wide configuration. To configure project or folder specific Mascot support:
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.
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).
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.
| previousnext |
| expand allcollapse all |
