Install databases and dependencies; checks and downloads all if necessary:
dammit install
Install databases:
dammit install-databases [--database-dir <dir>]
Install dependencies. Should there be an option for where to put them here?
dammit install-dependencies
Assess transcriptome. Runs BUSCO and basic stats. If it fails because of a
BUSCO database dependency check, inform the user of the subcommand necessary
to retrieve only the necessary database with dammit install-databases:
dammit assess -i <transcriptome.fasta> -o <output_dir> --busco-group <group>
Annotate transcriptome. If it fails due to a dependency check, inform the suer of the necessary subcommand:
dammit annotate -i <transcriptome.fasta> -o <output_dir> [--full]
Assess and annotate. Above two necessities apply:
dammit all -i <transcriptome.fasta> -i <output_dir> --busco-group <group> [--full]
- Need to decide whether to manage install with doit or a more traditional build system.
- It really should try to use system-available programs first.