|The GCG Sequence Analysis Package|
GCG is the Genetics Computer Group, also known as the Wisconsin Package. It's been around since 1982 with continuing support and upgrades until 2007. Accelrys, Inc., the present owner, has decided to 'retire' the package in June 2008, though FSU will continue to have the package available to users until it becomes incompatible with the Linux operating system on HPC. Unfortunately there is no way of knowing when that will happen.
The package consists of nearly 150 different, interrelated programs that can all work together to provide sophisticated research results. The X11 based SeqLab graphical user interface (GUI) provides a common sequence editing environment from which most of the programs can be run. The Program Manual is here, and I have created several workshops that can help you learn how to use the system at FSU.
Using GCG on HPC
GCG is now available on all HPC nodes since Accelrys has released the node-lock on the license with the package's retirement. GCG will not automatically initialize because only a subset of HPC users will be interested in its use. However, it is initialized by the activation of the Bio Roll. Therefore, depending on your shell, activate the Bio Roll with the following command. Respectively, for bash:
And for tcsh:
These commands could be put at the bottom of your .bashrc or .login file, respectively, to automatically activate all of the Bio Roll as well as GCG, or . . .
Alternatively, if you do not want to activate all of the Bio Roll but still want to use GCG, you can just initialize GCG by issuing the following commands, respectively, for bash:
. /opt/Bio/GCG/gcgstartup.ksh gcg
Or, with tcsh:
source /opt/Bio/GCG/gcgstartup gcg
Either of which could be put at the bottom of your .bashrc or .login file, respectively, in your account, so that you would only automatically initialize GCG.
To get your old data from the previous Mendel installation, recursively copy all of your old files from the directory in the shared HPC directory/panfs/storage.local/bio/mendel_user_data that corresponds to your previous Mendel login name. You may want to consider creating a new directory in your account for this:
mkdir old_mendel_data cp -r /panfs/storage.local/bio/mendel_user_data/old_id old_mendel_data
Where your new HPC account directory is named "old_mendel_data," and you substitute your old Mendel login name for "old_id."
Your old SeqLab list files that contain pointers to files in your account will no longer work on the HPC. The paths are incorrect in them. Either recreate them from scratch in SeqLab, or use an editor to change the path designations. Speaking of editors, pico is not installed, but nano is, and it works exactly the same as pico (emacs and vi are also there).