Refgenie

Fixed
- A bug with setuptools no longer allowing use_2to3.

Added
- _MapReduce_ framework support in `refgenie build` that supports automating asset builds at scale (`--map` and `--reduce` options)
- an option to automatically pull parent assets when building a derived asset (`--pull-parents` option in `refgenie build`)

Fixed
- misleading exit codes in `refgenie build`; [258](https://github.com/refgenie/refgenie/issues/258)

Added
- remote commands, which work without genome config file:
- `refgenie seekr`
- `refgenie populater`
- `refgenie listr`
- `refgenie populate` command for refgenie registry paths populating with local paths
- `--flag-meanings` argument to `refgenie compare` command

Changed

- instead of using human-readable names as genome identifiers refgenie uses sequence-derived digests in the config
- asset data moved to `data` directory
- asset files are now named after genome digests
- refgenieserver API v3 is now used for remote assets retrieval
- improved visual interface in `list`, `listr` and `pull` subcommands

Added

- `data` and `alias` directories in genome directory that are used to store asset and aliases data, respectively
- `refgenie alias` command for genome aliases management
- `refgenie upgrade` command for config format upgrades
- `refgenie compare` command for genome compatibility determination

Changed
- short option string for `--no-overwrite` from `-n` to `-o`

Added
- option to handle large asset archives pulling from the CLI (`-l`/`--no-large` flag)
- option to set the maximum archive size to `pull` with no confirmation required (`--size-cutoff` argument)
- `-s`/`--seek-keys` argument to `refgenie add` to specify seek keys for added assets

Fixed
- `refgenie add` issues -- added assets are no longer imported to the `genome_folder`; [180](https://github.com/refgenie/refgenie/issues/180)

Changed
- in `refgenie build` reduced the config file locking time to prevent problems in multi-build context
- dropped Python 2 support

Added
- parametrized `kmer` in salmon recipes
- support for all genome configuration file parameter values initialization in `refgenie init`