[ ] Change Rakefile to a script to create chain file that reads flo_opts.yaml as before. If config file does not exist, run on tmp/source.fa and tmp/target.fa using current BLAT options and using as many cpus as available.
[ ] Instead of trying to automatically lift over the given file, provide the liftOver command that is currently run in the README file.
[ ] Instead of automatically running gff_recover.rb, suggest its use in a section titled 'Lifting over GFF files'. Also, mention gff_remove and gff_longest_transcript in the same section.
[ ] In README, provide steps for creating synteny maps for use with ALLMAPS.
In addition to #22, provide:
tmp/source.faandtmp/target.fausing current BLAT options and using as many cpus as available.