`cores` is a required param introduced by Deep Genome Core
commits fe8805077131308b9fe1d335c and 09e020ffac5fc8045e0e3

more_itertools<=2.2's chunked() causes infinite loop sometimes

They are now inlined into the log file by the finalise.sh
script (not part of this repo)

First any single trailing * is stripped, then if there are still * in the
sequence, an error is raised. Previously, this was only done in the PhyML step.

- Cause: orthomcl._find_pairs did not cache invalidate when _create_database reran
- Solution: pass database creation date to _find_pairs.

This improves cache hits when adding a new species.

Split filtered orthomcl fasta of all species and feed each split fasta
to Blast2GO. Finally, output annotations per species, as well as for all
species together.

Also strip 'abbrev|' prefix from filtered fasta files and OrthoMCL
gene_families.txt output.

- Fixed and manually tested Blast2GO
- Decypher Blast instead of NCBI Blast
- Organise result into single directory of symlinks.

Apply chicken turtle project structure. Rename deep_blue_genome -> deep_genome. Refactor up to PhyML and Blast2GO (exclusive)

The pipeline code written by Jan Deneweth, with passwords replaced by
TODO_* as the repository will be made public.