In order to execute Perl scripts through JAMS, a Perl Execution Method must first be created. To do this, open the Execution Methods shortcut and click the +Add button from the Ribbon Bar. Name the Execution Method Perl, and choose the Execution Type SSHAgent. Toggle the checkbox to Edit the Execution Method Definition after Creating it.
Here, under the Execution Tab use the command JAMSAgentX or possibly the full path to the JAMSAgentX binary on the Linux node if it's not stored within /usr/bin/. The Type should already be set as SSH Agent.
In the Template Tab, add these lines:
#!/usr/bin/env perl <<JAMS.Source>> print "\n";
This will allow for any Perl script to be ran as a native JAMS Job without requiring the source to be saved and called as a Shell Script on Linux. This same method can be utilized for running nearly any script language, whether it's Perl as demonstrated here, PHP, Ruby or more.