do not use external FASTA splitter

instead use own Lua implementation
adjust CEGMA queue
adjust GMS queue
work around bug in CEGMA

CEGMA won't process sequences with pipe symbols ('|') in the header.
Replacing them with placeholders to circumvent this.
add ABACAS as step 0

Will not work outside Sanger Pathogens infrastructure as ABACAS2 was never
officially released/packaged and is not available stand-alone.
TMHMM: error checking
copyrights
add new configuration items in config.sh
orthomcl: error checking (WIP)
add RNA search submit script
add merge script to create comprehensive GFF with structural annotation