thorium: fix gcc compilation warnings

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
transport: move thorium configuration settings in a configuration file

Reduction of 30 s (it was 00:02:10 before).

time ./scripts/assembly_debugging/spate-saureus-fasta-gz-4x8.sh
1m42.484s

Link: https://github.com/GeneAssembly/biosal/issues/751
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>