Enable user databases, busco databases

[bluegenes]

• add shmlast rule & wrapper
• add busco v4 rule
• enable user database targets in app.py

[bluegenes]

both nominally working. Test with: dammitall annotate --database-dir tests/databases tests/test-data/pom.50.fa -o test_dammit_quick --n_threads 4 --pipeline quick --user-databases tests/databases/uniprot_sprot.fasta --busco-groups eukaryota_odb10

Note this cmd relies on databases installed at tests/databases, as it uses the uniprot database as a fake user database. Change this as needed. Other busco db's not enabled until we remove command line checks based on the databases.yml file.

If we build a custom config.ini file for busco, we can pass the config to the busco wrapper to alter the location for busco downloads (and direct output, rather than cp output as we currently do). However, the config file needs to contain all default info in addition to the changed info.

Params to modify: download_path = ./busco_downloads/ out_path = /path/to/output

busco user guide config info here and here