switch git repos to test merging of ur, gms-core, and workflow
change git clone syntax to work with a branch instead of a tag
add cpan update of Module::Runtime, synchronize TGI and sGMS environment variables
change method for retrieving public pgp key for cran from ubuntu
stop moving git repos
add instrument.fragment_library.bisulfite_conversion
update schema to include model.created_by and model.run_as
Merge branch 'ubuntu-12.04' into ubuntu-12.04-testmerge3
Switch /etc/genome.conf GENOME_SYS_GROUP from "info" to "genome".  Disable unused vars.
re-enabled environment vars for alternate dbs to point to default db
add workflow queue to lsb.queues
update paths to use new FTP site
update URL to FTP staging site
update apache conf to mount /opt/gms/ at /data/
update schema

a new schema dump was made from the TGI using pg_dump. Updated tables are
used for all schemas except for workflow. For the workflow schema, everything
was copied over from the previous dump.
Merge branch 'ubuntu-12.04-testmerge3' of github.com:genome/gms into ubuntu-12.04-testmerge3
increase result.software_result field version from character 64 to 1000
add code to prime timeline allocations in updated schema, now run in make targets where disk allocations are being primed
add new db priming to targets where disk allocations are being primed
set default nomenclature to GMS