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| The HPC Bio Roll: GCG and GNU bioinformatics |
The FSU HPC facility supports a large number of bioinformatics applications. Some of these come as a part of the standard "Rocks Bio Roll;" plus several other public domain applications, as well as the commercial GCG Wisconsin Package software suite, have been added to our HPC Bio Roll.
Using the Bioinformatics Suite on HPCThe Bioinformatics Suite is not initialized automatically upon logon. To activate the complete suite execute the /usr/local/profile.d/bio.sh or /usr/local/profile.d/bio.csh script depending on your shell, bash and tcsh respectively. These scripts can be sourced automatically by your logon by adding the following command to the bottom of your .bashrc or .login file, respecitively, for bash:
for tcsh:
These scripts will establish the $PATH environment variable to all of the bioinformatics binaries; will create a .ncbirc file and .t_coffee directory, if you don't already have them; and will activate the GCG package, if you are logged into submit.hpc.fsu.edu interactively. Furthermore, you need to be a member of the "biouser" group to access the GCG based databases on HPC. These include GenBank, UniProt, PROSITE, RefSeq, etc. If you are not in the "biouser" group, and you wish to access these databases, please contact Steve Thompson or any other member of the HPC support staff. |