IDEA (Interactive Display for Evolutionary Analyses) is a graphical interface for PAML (Yang, Z., 1997), a popular package for conducting molecular evolution analyses on phylogenies and associated sequences.
These notes were made when the HPC was running Rocks 4.1, so they may or may not work the same way after the cluster is upgraded to Rocks 5.2. You may find want to make sure the pre-requisites are installed before going on. The IDEA website has documentation but the installation literature is VERY limited! The documentation for downloading and installing is on IDEA's sourceforge website here.
For whatever reasons, the installer is a bit picky, so don't run it as root! We "install" it in a regular user's home folder first, and then move it to another location where other users can use it. Remember, don't use sudo to run the installer script!
Congratulations!  You have successfully installed IDEA.
You may find it convenient to add /export/home/alan/idea to your path for easy access to IDEA.
SGE event logs will be stored in /export/home/alan/idea/wf/event-logs.
This directory should be cleaned out periodically.
The script delete-old-event-logs may be used for this purpose.
IDEA uses the Workflow process management system to manage grid submissions.
The scripts /export/home/alan/idea/wf/bin/prolog_uninitialized and /export/home/alan/idea/wf/bin/epilog_uninitialized must be installed as prolog and epilog, respectively, on every queue on which Workflow jobs will be executed.
Grid submissions have been temporarily disabled.
You may still use IDEA, but all processes will be executed on the machine from which you launch IDEA.
Once an administrator has installed these scripts, rename /export/home/alan/idea/wf/bin/prolog_uninitialized to /export/home/alan/idea/wf/bin/prolog and /export/home/alan/idea/wf/bin/epilog_uninitialized to /export/home/alan/idea/wf/bin/epilog to enable grid submissions.
The program has a funny installer, as the software package isn't really "installed" (it's more like "configured"). This has the unfortunate side effect of putting lots of static references to the user's home directory where it was "installed."
Replace all instances of "home/alan" with "paracel/biosoft" so that the program runs correctly when we move it to its new location.